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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

All alleles are reported in the Forward orientation. Click on the Variant Details tab for details on Genomic Placement, Gene, and Amino Acid changes. HGVS names are in the HGVS tab.

Reference SNP (rs) Report

This page reports data for a single dbSNP Reference SNP variation (RefSNP or rs) from the new redesigned dbSNP build.
Top of the page reports a concise summary for the rs, with more specific details included in the corresponding tabs below.
All alleles are reported in the Forward orientation. Use the Genomic View to inspect the nucleotides flanking the variant, and its neighbors.
For more information see Help documentation.

rs10482719

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:218346587-218346592 (GRCh38.p14) Help

The anchor position for this RefSNP. Includes all nucleotides potentially affected by this change, thus it can differ from HGVS, which is right-shifted. See here for details.

Alleles
delACAA / dupACAA
Variation Type
Indel Insertion and Deletion
Frequency
dupACAA=0.390096 (54523/139768, GnomAD)
dupACAA=0.33894 (9577/28256, 14KJPN)
dupACAA=0.30935 (6117/19774, ALFA) (+ 10 more)
dupACAA=0.34016 (5701/16760, 8.3KJPN)
dupACAA=0.4258 (2727/6404, 1000G_30x)
dupACAA=0.4239 (2123/5008, 1000G)
dupACAA=0.2473 (1108/4480, Estonian)
dupACAA=0.2605 (1004/3854, ALSPAC)
dupACAA=0.2945 (1092/3708, TWINSUK)
dupACAA=0.3472 (636/1832, Korea1K)
dupACAA=0.319 (318/998, GoNL)
dupACAA=0.220 (132/600, NorthernSweden)
dupACAA=0.25 (10/40, GENOME_DK)
Clinical Significance
Reported in ClinVar
Gene : Consequence
TGFB2 : Non Coding Transcript Variant
TGFB2-AS1 : 2KB Upstream Variant
Publications
0 citations
Genomic View
See rs on genome

ALFA Allele Frequency
The ALFA project provide aggregate allele frequency from dbGaP. More information is available on the project page including descriptions, data access, and terms of use.

Release Version: 20230706150541
Population Group Sample Size Ref Allele Alt Allele
Total Global 19774 AAACAA=0.69065 AAACAAACAA=0.30935
European Sub 15522 AAACAA=0.74552 AAACAAACAA=0.25448
African Sub 2816 AAACAA=0.4038 AAACAAACAA=0.5962
African Others Sub 108 AAACAA=0.306 AAACAAACAA=0.694
African American Sub 2708 AAACAA=0.4077 AAACAAACAA=0.5923
Asian Sub 108 AAACAA=0.667 AAACAAACAA=0.333
East Asian Sub 84 AAACAA=0.65 AAACAAACAA=0.35
Other Asian Sub 24 AAACAA=0.71 AAACAAACAA=0.29
Latin American 1 Sub 146 AAACAA=0.637 AAACAAACAA=0.363
Latin American 2 Sub 610 AAACAA=0.679 AAACAAACAA=0.321
South Asian Sub 94 AAACAA=0.71 AAACAAACAA=0.29
Other Sub 478 AAACAA=0.632 AAACAAACAA=0.368


Help

Frequency tab displays a table of the reference and alternate allele frequencies reported by various studies and populations. Table lines, where Population="Global" refer to the entire study population, whereas lines, where Group="Sub", refer to a study-specific population subgroupings (i.e. AFR, CAU, etc.), if available. Frequency for the alternate allele (Alt Allele) is a ratio of samples observed-to-total, where the numerator (observed samples) is the number of chromosomes in the study with the minor allele present (found in "Sample size", where Group="Sub"), and the denominator (total samples) is the total number of all chromosomes in the study for the variant (found in "Sample size", where Group="Study-wide" and Population="Global").

Download
Study Population Group Sample Size Ref Allele Alt Allele
gnomAD - Genomes Global Study-wide 139768 -

No frequency provided

dupACAA=0.390096
gnomAD - Genomes European Sub 75758 -

No frequency provided

dupACAA=0.27320
gnomAD - Genomes African Sub 41772 -

No frequency provided

dupACAA=0.64232
gnomAD - Genomes American Sub 13644 -

No frequency provided

dupACAA=0.29148
gnomAD - Genomes Ashkenazi Jewish Sub 3316 -

No frequency provided

dupACAA=0.3139
gnomAD - Genomes East Asian Sub 3126 -

No frequency provided

dupACAA=0.3832
gnomAD - Genomes Other Sub 2152 -

No frequency provided

dupACAA=0.3620
14KJPN JAPANESE Study-wide 28256 -

No frequency provided

dupACAA=0.33894
Allele Frequency Aggregator Total Global 19774 AAACAA=0.69065 dupACAA=0.30935
Allele Frequency Aggregator European Sub 15522 AAACAA=0.74552 dupACAA=0.25448
Allele Frequency Aggregator African Sub 2816 AAACAA=0.4038 dupACAA=0.5962
Allele Frequency Aggregator Latin American 2 Sub 610 AAACAA=0.679 dupACAA=0.321
Allele Frequency Aggregator Other Sub 478 AAACAA=0.632 dupACAA=0.368
Allele Frequency Aggregator Latin American 1 Sub 146 AAACAA=0.637 dupACAA=0.363
Allele Frequency Aggregator Asian Sub 108 AAACAA=0.667 dupACAA=0.333
Allele Frequency Aggregator South Asian Sub 94 AAACAA=0.71 dupACAA=0.29
8.3KJPN JAPANESE Study-wide 16760 -

No frequency provided

dupACAA=0.34016
1000Genomes_30x Global Study-wide 6404 -

No frequency provided

dupACAA=0.4258
1000Genomes_30x African Sub 1786 -

No frequency provided

dupACAA=0.6865
1000Genomes_30x Europe Sub 1266 -

No frequency provided

dupACAA=0.2725
1000Genomes_30x South Asian Sub 1202 -

No frequency provided

dupACAA=0.3636
1000Genomes_30x East Asian Sub 1170 -

No frequency provided

dupACAA=0.3735
1000Genomes_30x American Sub 980 -

No frequency provided

dupACAA=0.288
1000Genomes Global Study-wide 5008 -

No frequency provided

dupACAA=0.4239
1000Genomes African Sub 1322 -

No frequency provided

dupACAA=0.6831
1000Genomes East Asian Sub 1008 -

No frequency provided

dupACAA=0.3819
1000Genomes Europe Sub 1006 -

No frequency provided

dupACAA=0.2704
1000Genomes South Asian Sub 978 -

No frequency provided

dupACAA=0.369
1000Genomes American Sub 694 -

No frequency provided

dupACAA=0.291
Genetic variation in the Estonian population Estonian Study-wide 4480 -

No frequency provided

dupACAA=0.2473
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 -

No frequency provided

dupACAA=0.2605
UK 10K study - Twins TWIN COHORT Study-wide 3708 -

No frequency provided

dupACAA=0.2945
Korean Genome Project KOREAN Study-wide 1832 -

No frequency provided

dupACAA=0.3472
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 -

No frequency provided

dupACAA=0.319
Northern Sweden ACPOP Study-wide 600 -

No frequency provided

dupACAA=0.220
The Danish reference pan genome Danish Study-wide 40 -

No frequency provided

dupACAA=0.25
Help

Variant Details tab shows known variant placements on genomic sequences: chromosomes (NC_), RefSeqGene, pseudogenes or genomic regions (NG_), and in a separate table: on transcripts (NM_) and protein sequences (NP_). The corresponding transcript and protein locations are listed in adjacent lines, along with molecular consequences from Sequence Ontology. When no protein placement is available, only the transcript is listed. Column "Codon[Amino acid]" shows the actual base change in the format of "Reference > Alternate" allele, including the nucleotide codon change in transcripts, and the amino acid change in proteins, respectively, allowing for known ribosomal slippage sites. To view nucleotides adjacent to the variant use the Genomic View at the bottom of the page - zoom into the sequence until the nucleotides around the variant become visible.

Genomic Placements
Sequence name Change
GRCh38.p14 chr 1 NC_000001.11:g.218346589_218346592del
GRCh38.p14 chr 1 NC_000001.11:g.218346589_218346592dup
GRCh37.p13 chr 1 NC_000001.10:g.218519931_218519934del
GRCh37.p13 chr 1 NC_000001.10:g.218519931_218519934dup
TGFB2 RefSeqGene NG_027721.2:g.6256_6259del
TGFB2 RefSeqGene NG_027721.2:g.6256_6259dup
Gene: TGFB2, transforming growth factor beta 2 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
TGFB2 transcript variant 2 NM_003238.6:c.-115_-110= N/A 5 Prime UTR Variant
TGFB2 transcript variant 1 NM_001135599.4:c.-115_-11…

NM_001135599.4:c.-115_-110=

N/A 5 Prime UTR Variant
TGFB2 transcript variant 3 NR_138148.2:n.1254_1257del N/A Non Coding Transcript Variant
TGFB2 transcript variant 3 NR_138148.2:n.1254_1257dup N/A Non Coding Transcript Variant
TGFB2 transcript variant 4 NR_138149.2:n.1254_1257del N/A Non Coding Transcript Variant
TGFB2 transcript variant 4 NR_138149.2:n.1254_1257dup N/A Non Coding Transcript Variant
Gene: TGFB2-AS1, TGFB2 antisense RNA 1 (head to head) (minus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
TGFB2-AS1 transcript NR_046268.1:n. N/A Upstream Transcript Variant
Help

Clinical Significance tab shows a list of clinical significance entries from ClinVar associated with the variation, per allele. Click on the RCV accession (i.e. RCV000001615.2) or Allele ID (i.e. 12274) to access full ClinVar report.

Allele: dupACAA (allele ID: 279220 )
ClinVar Accession Disease Names Clinical Significance
RCV000349662.3 Loeys-Dietz syndrome Benign
RCV001711770.1 not provided Benign
Help

Aliases tab displays HGVS names representing the variant placements and allele changes on genomic, transcript and protein sequences, per allele. HGVS name is an expression for reporting sequence accession and version, sequence type, position, and allele change. The column "Note" can have two values: "diff" means that there is a difference between the reference allele (variation interval) at the placement reported in HGVS name and the reference alleles reported in other HGVS names, and "rev" means that the sequence of this variation interval at the placement reported in HGVS name is in reverse orientation to the sequence(s) of this variation in other HGVS names not labeled as "rev".

Placement AAACAA= delACAA dupACAA
GRCh38.p14 chr 1 NC_000001.11:g.218346587_218346592= NC_000001.11:g.218346589_218346592del NC_000001.11:g.218346589_218346592dup
GRCh37.p13 chr 1 NC_000001.10:g.218519929_218519934= NC_000001.10:g.218519931_218519934del NC_000001.10:g.218519931_218519934dup
TGFB2 RefSeqGene NG_027721.2:g.6254_6259= NG_027721.2:g.6256_6259del NG_027721.2:g.6256_6259dup
TGFB2 transcript variant 2 NM_003238.6:c.-115_-110= NM_003238.6:c.-113_-110del NM_003238.6:c.-113_-110dup
TGFB2 transcript variant 2 NM_003238.5:c.-115_-110= NM_003238.5:c.-113_-110del NM_003238.5:c.-113_-110dup
TGFB2 transcript variant 2 NM_003238.4:c.-115_-110= NM_003238.4:c.-113_-110del NM_003238.4:c.-113_-110dup
TGFB2 transcript variant 2 NM_003238.3:c.-115_-110= NM_003238.3:c.-113_-110del NM_003238.3:c.-113_-110dup
TGFB2 transcript variant 1 NM_001135599.4:c.-115_-110= NM_001135599.4:c.-113_-110del NM_001135599.4:c.-113_-110dup
TGFB2 transcript variant 1 NM_001135599.3:c.-115_-110= NM_001135599.3:c.-113_-110del NM_001135599.3:c.-113_-110dup
TGFB2 transcript variant 1 NM_001135599.2:c.-115_-110= NM_001135599.2:c.-113_-110del NM_001135599.2:c.-113_-110dup
TGFB2 transcript variant 4 NR_138149.2:n.1252_1257= NR_138149.2:n.1254_1257del NR_138149.2:n.1254_1257dup
TGFB2 transcript variant 4 NR_138149.1:n.1304_1309= NR_138149.1:n.1306_1309del NR_138149.1:n.1306_1309dup
TGFB2 transcript variant 3 NR_138148.2:n.1252_1257= NR_138148.2:n.1254_1257del NR_138148.2:n.1254_1257dup
TGFB2 transcript variant 3 NR_138148.1:n.1304_1309= NR_138148.1:n.1306_1309del NR_138148.1:n.1306_1309dup
Help

Submissions tab displays variations originally submitted to dbSNP, now supporting this RefSNP cluster (rs). We display Submitter handle, Submission identifier, Date and Build number, when the submission appeared for the first time. Direct submissions to dbSNP have Submission ID in the form of an ss-prefixed number (ss#). Other supporting variations are listed in the table without ss#.

69 SubSNP, 13 Frequency, 2 ClinVar submissions
No Submitter Submission ID Date (Build)
1 EGP_SNPS ss14865866 Dec 03, 2013 (142)
2 IIPGA-WEISS-MARTINEZ ss15356601 Feb 28, 2004 (120)
3 KYUGEN ss28459794 Oct 11, 2018 (152)
4 KYUGEN ss28460694 Dec 03, 2013 (142)
5 HGSV ss80967953 Dec 04, 2013 (142)
6 GI-BIOTEC ss86354044 Dec 05, 2013 (142)
7 ILLUMINA ss107694429 Dec 06, 2013 (142)
8 ILLUMINA ss159898103 Dec 01, 2009 (131)
9 ILLUMINA ss170139352 Dec 06, 2013 (142)
10 BUSHMAN ss193151337 Jul 04, 2010 (132)
11 GMI ss288093296 May 04, 2012 (137)
12 1000GENOMES ss326134462 May 09, 2011 (135)
13 1000GENOMES ss326139944 May 09, 2011 (135)
14 1000GENOMES ss326183429 May 09, 2011 (135)
15 ILLUMINA ss479658255 Oct 11, 2018 (152)
16 ILLUMINA ss536609136 Oct 11, 2018 (152)
17 LUNTER ss551022042 Apr 25, 2013 (138)
18 LUNTER ss551052794 Apr 25, 2013 (138)
19 LUNTER ss552844634 Apr 25, 2013 (138)
20 TISHKOFF ss554746726 Apr 25, 2013 (138)
21 SSMP ss663158268 Apr 01, 2015 (144)
22 EVA-GONL ss976156828 Aug 21, 2014 (142)
23 1000GENOMES ss1368004965 Aug 21, 2014 (142)
24 DDI ss1536265346 Apr 01, 2015 (144)
25 EVA_GENOME_DK ss1574094924 Apr 01, 2015 (144)
26 EVA_DECODE ss1585553362 Apr 01, 2015 (144)
27 EVA_UK10K_ALSPAC ss1701794539 Apr 01, 2015 (144)
28 EVA_UK10K_TWINSUK ss1701795058 Apr 01, 2015 (144)
29 HAMMER_LAB ss1795745520 Sep 08, 2015 (146)
30 JJLAB ss2030376488 Sep 14, 2016 (149)
31 SYSTEMSBIOZJU ss2624615680 Nov 08, 2017 (151)
32 SWEGEN ss2988468431 Nov 08, 2017 (151)
33 MCHAISSO ss3063626499 Nov 08, 2017 (151)
34 MCHAISSO ss3065350512 Nov 08, 2017 (151)
35 ILLUMINA ss3626311757 Oct 11, 2018 (152)
36 ILLUMINA ss3636052499 Oct 11, 2018 (152)
37 ILLUMINA ss3637814938 Oct 11, 2018 (152)
38 ILLUMINA ss3642821253 Oct 11, 2018 (152)
39 BEROUKHIMLAB ss3644078717 Oct 11, 2018 (152)
40 BIOINF_KMB_FNS_UNIBA ss3645098172 Oct 11, 2018 (152)
41 EGCUT_WGS ss3656429673 Jul 12, 2019 (153)
42 EVA_DECODE ss3688651555 Jul 12, 2019 (153)
43 ACPOP ss3727872564 Jul 12, 2019 (153)
44 KHV_HUMAN_GENOMES ss3800353550 Jul 12, 2019 (153)
45 EVA ss3826649447 Apr 25, 2020 (154)
46 EVA ss3836725154 Apr 25, 2020 (154)
47 EVA ss3842137052 Apr 25, 2020 (154)
48 KOGIC ss3946512307 Apr 25, 2020 (154)
49 FSA-LAB ss3983963446 Apr 25, 2021 (155)
50 FSA-LAB ss3983963447 Apr 25, 2021 (155)
51 FSA-LAB ss3983963448 Apr 25, 2021 (155)
52 EVA ss3986015519 Apr 25, 2021 (155)
53 EVA ss3986159359 Apr 25, 2021 (155)
54 GNOMAD ss4011490230 Apr 25, 2021 (155)
55 TOMMO_GENOMICS ss5148478369 Apr 25, 2021 (155)
56 1000G_HIGH_COVERAGE ss5245834758 Oct 12, 2022 (156)
57 HUGCELL_USP ss5446269885 Oct 12, 2022 (156)
58 EVA ss5506190617 Oct 12, 2022 (156)
59 1000G_HIGH_COVERAGE ss5519953371 Oct 12, 2022 (156)
60 EVA ss5624003134 Oct 12, 2022 (156)
61 SANFORD_IMAGENETICS ss5627471225 Oct 12, 2022 (156)
62 TOMMO_GENOMICS ss5676252520 Oct 12, 2022 (156)
63 EVA ss5800090060 Oct 12, 2022 (156)
64 YY_MCH ss5801646476 Oct 12, 2022 (156)
65 EVA ss5833276759 Oct 12, 2022 (156)
66 EVA ss5848285928 Oct 12, 2022 (156)
67 EVA ss5849289227 Oct 12, 2022 (156)
68 EVA ss5912020874 Oct 12, 2022 (156)
69 EVA ss5939309816 Oct 12, 2022 (156)
70 1000Genomes NC_000001.10 - 218519929 Oct 11, 2018 (152)
71 1000Genomes_30x NC_000001.11 - 218346587 Oct 12, 2022 (156)
72 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 218519929 Oct 11, 2018 (152)
73 Genetic variation in the Estonian population NC_000001.10 - 218519929 Oct 11, 2018 (152)
74 The Danish reference pan genome NC_000001.10 - 218519929 Apr 25, 2020 (154)
75 gnomAD - Genomes NC_000001.11 - 218346587 Apr 25, 2021 (155)
76 Genome of the Netherlands Release 5 NC_000001.10 - 218519929 Apr 25, 2020 (154)
77 Korean Genome Project NC_000001.11 - 218346587 Apr 25, 2020 (154)
78 Northern Sweden NC_000001.10 - 218519929 Jul 12, 2019 (153)
79 8.3KJPN NC_000001.10 - 218519929 Apr 25, 2021 (155)
80 14KJPN NC_000001.11 - 218346587 Oct 12, 2022 (156)
81 UK 10K study - Twins NC_000001.10 - 218519929 Oct 11, 2018 (152)
82 ALFA NC_000001.11 - 218346587 Apr 25, 2021 (155)
83 ClinVar RCV000349662.3 Oct 12, 2022 (156)
84 ClinVar RCV001711770.1 Oct 12, 2022 (156)
Help

History tab displays RefSNPs (Associated ID) from previous builds (Build) that now support the current RefSNP, and the dates, when the history was updated for each Associated ID (History Updated).

Associated ID History Updated (Build)
rs59852755 May 25, 2008 (130)
rs113490720 May 15, 2013 (138)
rs386513269 Aug 21, 2014 (142)
rs397725404 Aug 21, 2014 (142)
rs147577544 Sep 17, 2011 (135)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss5506190617 NC_000001.10:218519928:AAAC: NC_000001.11:218346586:AAACAA:AA
ss326134462, ss326139944, ss326183429, ss551022042, ss551052794, ss552844634, ss1585553362 NC_000001.9:216586551::AAAC NC_000001.11:218346586:AAACAA:AAAC…

NC_000001.11:218346586:AAACAA:AAACAAACAA

(self)
ss159898103, ss288093296, ss3642821253 NC_000001.9:216586557::ACAA NC_000001.11:218346586:AAACAA:AAAC…

NC_000001.11:218346586:AAACAA:AAACAAACAA

(self)
5551188, 3066033, 2167921, 200591, 1339819, 1157429, 6447676, 3066033, ss663158268, ss976156828, ss1368004965, ss1536265346, ss1574094924, ss1701794539, ss1701795058, ss1795745520, ss2030376488, ss2624615680, ss2988468431, ss3644078717, ss3656429673, ss3727872564, ss3826649447, ss3836725154, ss3983963446, ss3986015519, ss3986159359, ss5148478369, ss5624003134, ss5627471225, ss5800090060, ss5833276759, ss5939309816 NC_000001.10:218519928::AAAC NC_000001.11:218346586:AAACAA:AAAC…

NC_000001.11:218346586:AAACAA:AAACAAACAA

(self)
ss479658255, ss536609136, ss554746726, ss3626311757, ss3636052499, ss3637814938, ss3983963447, ss3983963448, ss5848285928 NC_000001.10:218519934::ACAA NC_000001.11:218346586:AAACAA:AAAC…

NC_000001.11:218346586:AAACAA:AAACAAACAA

(self)
7479306, 39890696, 2890308, 10089624, ss3063626499, ss3065350512, ss3645098172, ss3688651555, ss3800353550, ss3842137052, ss3946512307, ss4011490230, ss5245834758, ss5446269885, ss5519953371, ss5676252520, ss5801646476, ss5849289227, ss5912020874 NC_000001.11:218346586::AAAC NC_000001.11:218346586:AAACAA:AAAC…

NC_000001.11:218346586:AAACAA:AAACAAACAA

(self)
RCV000349662.3, RCV001711770.1, 4095294022 NC_000001.11:218346586:AAACAA:AAAC…

NC_000001.11:218346586:AAACAA:AAACAAACAA

NC_000001.11:218346586:AAACAA:AAAC…

NC_000001.11:218346586:AAACAA:AAACAAACAA

(self)
ss193151337 NT_004487.20:75161999::AAAC NC_000001.11:218346586:AAACAA:AAAC…

NC_000001.11:218346586:AAACAA:AAACAAACAA

(self)
ss15356601 NT_167186.1:12037710::CAAA NC_000001.11:218346586:AAACAA:AAAC…

NC_000001.11:218346586:AAACAA:AAACAAACAA

(self)
ss28459794 NT_167186.1:12037711::AAAC NC_000001.11:218346586:AAACAA:AAAC…

NC_000001.11:218346586:AAACAA:AAACAAACAA

(self)
ss14865866, ss28460694, ss80967953, ss86354044, ss107694429, ss170139352 NT_167186.1:12037713::ACAA NC_000001.11:218346586:AAACAA:AAAC…

NC_000001.11:218346586:AAACAA:AAACAAACAA

(self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs10482719

Help

The Flanks tab provides retrieving flanking sequences of a SNP on all molecules that have placements.

Genome context:
Select flank length:

Genomic regions, transcripts, and products
Top Help

NCBI Graphical Sequence Viewer display of the genomic region, transcripts and protein products for the reported RefSNP (rs).
Use the zoom option to view the nucleotides around the RefSNP and find other neighboring RefSNPs.
Visit Sequence Viewer for help with navigating inside the display and modifying the selection of displayed data tracks.

Software version is: 2.0.1.post761+d5e8e07