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dbSNP Short Genetic Variations

Examples: rs268, BRCA1 and more Advanced search

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.

rs2245697

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr11:102624013 (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
G>A
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.263822 (69831/264690, TOPMED)
G=0.264458 (37077/140200, GnomAD)
G=0.08992 (2541/28258, 14KJPN) (+ 16 more)
G=0.25717 (4858/18890, ALFA)
G=0.09154 (1534/16758, 8.3KJPN)
G=0.2539 (1626/6404, 1000G_30x)
G=0.2490 (1247/5008, 1000G)
G=0.2458 (1101/4480, Estonian)
G=0.2247 (866/3854, ALSPAC)
G=0.2214 (821/3708, TWINSUK)
G=0.0956 (280/2930, KOREAN)
G=0.1015 (186/1832, Korea1K)
G=0.229 (229/998, GoNL)
G=0.243 (146/600, NorthernSweden)
G=0.128 (68/530, SGDP_PRJ)
G=0.241 (52/216, Qatari)
G=0.019 (4/212, Vietnamese)
G=0.07 (4/56, Siberian)
G=0.33 (13/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
MMP20 : Intron Variant
LOC101928477 : Intron 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 18890 G=0.25717 A=0.74283
European Sub 14286 G=0.23779 A=0.76221
African Sub 2946 G=0.3496 A=0.6504
African Others Sub 114 G=0.351 A=0.649
African American Sub 2832 G=0.3496 A=0.6504
Asian Sub 112 G=0.080 A=0.920
East Asian Sub 86 G=0.10 A=0.90
Other Asian Sub 26 G=0.00 A=1.00
Latin American 1 Sub 146 G=0.247 A=0.753
Latin American 2 Sub 610 G=0.269 A=0.731
South Asian Sub 98 G=0.17 A=0.83
Other Sub 692 G=0.296 A=0.704


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
TopMed Global Study-wide 264690 G=0.263822 A=0.736178
gnomAD - Genomes Global Study-wide 140200 G=0.264458 A=0.735542
gnomAD - Genomes European Sub 75918 G=0.22591 A=0.77409
gnomAD - Genomes African Sub 42010 G=0.35042 A=0.64958
gnomAD - Genomes American Sub 13662 G=0.24667 A=0.75333
gnomAD - Genomes Ashkenazi Jewish Sub 3324 G=0.3165 A=0.6835
gnomAD - Genomes East Asian Sub 3134 G=0.0807 A=0.9193
gnomAD - Genomes Other Sub 2152 G=0.2463 A=0.7537
14KJPN JAPANESE Study-wide 28258 G=0.08992 A=0.91008
Allele Frequency Aggregator Total Global 18890 G=0.25717 A=0.74283
Allele Frequency Aggregator European Sub 14286 G=0.23779 A=0.76221
Allele Frequency Aggregator African Sub 2946 G=0.3496 A=0.6504
Allele Frequency Aggregator Other Sub 692 G=0.296 A=0.704
Allele Frequency Aggregator Latin American 2 Sub 610 G=0.269 A=0.731
Allele Frequency Aggregator Latin American 1 Sub 146 G=0.247 A=0.753
Allele Frequency Aggregator Asian Sub 112 G=0.080 A=0.920
Allele Frequency Aggregator South Asian Sub 98 G=0.17 A=0.83
8.3KJPN JAPANESE Study-wide 16758 G=0.09154 A=0.90846
1000Genomes_30x Global Study-wide 6404 G=0.2539 A=0.7461
1000Genomes_30x African Sub 1786 G=0.3925 A=0.6075
1000Genomes_30x Europe Sub 1266 G=0.2480 A=0.7520
1000Genomes_30x South Asian Sub 1202 G=0.2130 A=0.7870
1000Genomes_30x East Asian Sub 1170 G=0.0974 A=0.9026
1000Genomes_30x American Sub 980 G=0.246 A=0.754
1000Genomes Global Study-wide 5008 G=0.2490 A=0.7510
1000Genomes African Sub 1322 G=0.3896 A=0.6104
1000Genomes East Asian Sub 1008 G=0.0962 A=0.9038
1000Genomes Europe Sub 1006 G=0.2465 A=0.7535
1000Genomes South Asian Sub 978 G=0.216 A=0.784
1000Genomes American Sub 694 G=0.254 A=0.746
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.2458 A=0.7542
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.2247 A=0.7753
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.2214 A=0.7786
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.0956 A=0.9044
Korean Genome Project KOREAN Study-wide 1832 G=0.1015 A=0.8985
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.229 A=0.771
Northern Sweden ACPOP Study-wide 600 G=0.243 A=0.757
SGDP_PRJ Global Study-wide 530 G=0.128 A=0.872
Qatari Global Study-wide 216 G=0.241 A=0.759
A Vietnamese Genetic Variation Database Global Study-wide 212 G=0.019 A=0.981
Siberian Global Study-wide 56 G=0.07 A=0.93
The Danish reference pan genome Danish Study-wide 40 G=0.33 A=0.68
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 11 NC_000011.10:g.102624013G>A
GRCh37.p13 chr 11 NC_000011.9:g.102494744G>A
MMP20 RefSeqGene NG_012151.1:g.6320C>T
Gene: MMP20, matrix metallopeptidase 20 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
MMP20 transcript NM_004771.4:c.126+1181C>T N/A Intron Variant
Gene: LOC101928477, uncharacterized LOC101928477 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LOC101928477 transcript variant X4 XR_001748340.2:n. N/A Intron Variant
LOC101928477 transcript variant X5 XR_001748341.2:n. N/A Genic Upstream Transcript Variant
LOC101928477 transcript variant X2 XR_007062866.1:n. N/A Genic Upstream Transcript Variant
LOC101928477 transcript variant X6 XR_007062867.1:n. N/A Genic Upstream Transcript Variant
LOC101928477 transcript variant X1 XR_947957.3:n. N/A Genic Upstream Transcript Variant
LOC101928477 transcript variant X3 XR_947958.3:n. N/A Genic 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.

Not Reported in ClinVar
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 G= A
GRCh38.p14 chr 11 NC_000011.10:g.102624013= NC_000011.10:g.102624013G>A
GRCh37.p13 chr 11 NC_000011.9:g.102494744= NC_000011.9:g.102494744G>A
MMP20 RefSeqGene NG_012151.1:g.6320= NG_012151.1:g.6320C>T
MMP20 transcript NM_004771.3:c.126+1181= NM_004771.3:c.126+1181C>T
MMP20 transcript NM_004771.4:c.126+1181= NM_004771.4:c.126+1181C>T
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#.

83 SubSNP, 19 Frequency submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss3374149 Sep 28, 2001 (100)
2 SC_JCM ss3454943 Sep 28, 2001 (100)
3 SC_SNP ss16123963 Feb 27, 2004 (120)
4 CSHL-HAPMAP ss17428224 Feb 27, 2004 (120)
5 CSHL-HAPMAP ss19206965 Feb 27, 2004 (120)
6 SSAHASNP ss20843447 Apr 05, 2004 (121)
7 EGP_SNPS ss28446759 Sep 20, 2004 (123)
8 ABI ss38690031 Mar 13, 2006 (126)
9 HGSV ss77246577 Dec 07, 2007 (129)
10 HGSV ss82274607 Dec 14, 2007 (130)
11 HGSV ss84617197 Dec 14, 2007 (130)
12 BCMHGSC_JDW ss88750483 Mar 24, 2008 (129)
13 HUMANGENOME_JCVI ss97506031 Feb 04, 2009 (130)
14 BGI ss106766195 Feb 04, 2009 (130)
15 1000GENOMES ss110972830 Jan 25, 2009 (130)
16 1000GENOMES ss115083299 Jan 25, 2009 (130)
17 ENSEMBL ss132784312 Dec 01, 2009 (131)
18 ENSEMBL ss137876631 Dec 01, 2009 (131)
19 GMI ss156720619 Dec 01, 2009 (131)
20 COMPLETE_GENOMICS ss168721443 Jul 04, 2010 (132)
21 COMPLETE_GENOMICS ss170778474 Jul 04, 2010 (132)
22 COMPLETE_GENOMICS ss175261020 Jul 04, 2010 (132)
23 BUSHMAN ss203134792 Jul 04, 2010 (132)
24 BCM-HGSC-SUB ss207549820 Jul 04, 2010 (132)
25 1000GENOMES ss225429073 Jul 14, 2010 (132)
26 1000GENOMES ss235695119 Jul 15, 2010 (132)
27 1000GENOMES ss242298144 Jul 15, 2010 (132)
28 BL ss255361435 May 09, 2011 (134)
29 GMI ss281148036 May 04, 2012 (137)
30 GMI ss286445453 Apr 25, 2013 (138)
31 PJP ss291126740 May 09, 2011 (134)
32 TISHKOFF ss562786816 Apr 25, 2013 (138)
33 SSMP ss658309396 Apr 25, 2013 (138)
34 EVA-GONL ss988898743 Aug 21, 2014 (142)
35 JMKIDD_LAB ss1077998038 Aug 21, 2014 (142)
36 1000GENOMES ss1342723504 Aug 21, 2014 (142)
37 DDI ss1426742622 Apr 01, 2015 (144)
38 EVA_GENOME_DK ss1575916062 Apr 01, 2015 (144)
39 EVA_DECODE ss1598562898 Apr 01, 2015 (144)
40 EVA_UK10K_ALSPAC ss1627331079 Apr 01, 2015 (144)
41 EVA_UK10K_TWINSUK ss1670325112 Apr 01, 2015 (144)
42 HAMMER_LAB ss1806969957 Sep 08, 2015 (146)
43 WEILL_CORNELL_DGM ss1932261350 Feb 12, 2016 (147)
44 GENOMED ss1967443183 Jul 19, 2016 (147)
45 JJLAB ss2026875008 Sep 14, 2016 (149)
46 USC_VALOUEV ss2155186790 Dec 20, 2016 (150)
47 HUMAN_LONGEVITY ss2185198723 Dec 20, 2016 (150)
48 SYSTEMSBIOZJU ss2627910716 Nov 08, 2017 (151)
49 GRF ss2699491501 Nov 08, 2017 (151)
50 GNOMAD ss2903770015 Nov 08, 2017 (151)
51 SWEGEN ss3008684252 Nov 08, 2017 (151)
52 BIOINF_KMB_FNS_UNIBA ss3027236170 Nov 08, 2017 (151)
53 CSHL ss3349766709 Nov 08, 2017 (151)
54 URBANLAB ss3649690755 Oct 12, 2018 (152)
55 EGCUT_WGS ss3676005864 Jul 13, 2019 (153)
56 EVA_DECODE ss3692482339 Jul 13, 2019 (153)
57 ACPOP ss3738488745 Jul 13, 2019 (153)
58 EVA ss3749736696 Jul 13, 2019 (153)
59 PACBIO ss3787050988 Jul 13, 2019 (153)
60 PACBIO ss3792177828 Jul 13, 2019 (153)
61 PACBIO ss3797060326 Jul 13, 2019 (153)
62 KHV_HUMAN_GENOMES ss3815070052 Jul 13, 2019 (153)
63 EVA ss3832808326 Apr 26, 2020 (154)
64 EVA ss3839965760 Apr 26, 2020 (154)
65 EVA ss3845446951 Apr 26, 2020 (154)
66 SGDP_PRJ ss3877014695 Apr 26, 2020 (154)
67 KRGDB ss3925455960 Apr 26, 2020 (154)
68 KOGIC ss3970631454 Apr 26, 2020 (154)
69 TOPMED ss4897827087 Apr 26, 2021 (155)
70 TOMMO_GENOMICS ss5203620457 Apr 26, 2021 (155)
71 1000G_HIGH_COVERAGE ss5288692138 Oct 16, 2022 (156)
72 EVA ss5401859571 Oct 16, 2022 (156)
73 HUGCELL_USP ss5483701825 Oct 16, 2022 (156)
74 EVA ss5510496292 Oct 16, 2022 (156)
75 1000G_HIGH_COVERAGE ss5585069612 Oct 16, 2022 (156)
76 SANFORD_IMAGENETICS ss5651953302 Oct 16, 2022 (156)
77 TOMMO_GENOMICS ss5751990931 Oct 16, 2022 (156)
78 YY_MCH ss5812726029 Oct 16, 2022 (156)
79 EVA ss5837146233 Oct 16, 2022 (156)
80 EVA ss5850125257 Oct 16, 2022 (156)
81 EVA ss5921412628 Oct 16, 2022 (156)
82 EVA ss5943275315 Oct 16, 2022 (156)
83 EVA ss5980699161 Oct 16, 2022 (156)
84 1000Genomes NC_000011.9 - 102494744 Oct 12, 2018 (152)
85 1000Genomes_30x NC_000011.10 - 102624013 Oct 16, 2022 (156)
86 The Avon Longitudinal Study of Parents and Children NC_000011.9 - 102494744 Oct 12, 2018 (152)
87 Genetic variation in the Estonian population NC_000011.9 - 102494744 Oct 12, 2018 (152)
88 The Danish reference pan genome NC_000011.9 - 102494744 Apr 26, 2020 (154)
89 gnomAD - Genomes NC_000011.10 - 102624013 Apr 26, 2021 (155)
90 Genome of the Netherlands Release 5 NC_000011.9 - 102494744 Apr 26, 2020 (154)
91 KOREAN population from KRGDB NC_000011.9 - 102494744 Apr 26, 2020 (154)
92 Korean Genome Project NC_000011.10 - 102624013 Apr 26, 2020 (154)
93 Northern Sweden NC_000011.9 - 102494744 Jul 13, 2019 (153)
94 Qatari NC_000011.9 - 102494744 Apr 26, 2020 (154)
95 SGDP_PRJ NC_000011.9 - 102494744 Apr 26, 2020 (154)
96 Siberian NC_000011.9 - 102494744 Apr 26, 2020 (154)
97 8.3KJPN NC_000011.9 - 102494744 Apr 26, 2021 (155)
98 14KJPN NC_000011.10 - 102624013 Oct 16, 2022 (156)
99 TopMed NC_000011.10 - 102624013 Apr 26, 2021 (155)
100 UK 10K study - Twins NC_000011.9 - 102494744 Oct 12, 2018 (152)
101 A Vietnamese Genetic Variation Database NC_000011.9 - 102494744 Jul 13, 2019 (153)
102 ALFA NC_000011.10 - 102624013 Apr 26, 2021 (155)
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)
rs17099137 Oct 08, 2004 (123)
rs57409119 May 23, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss77246577, ss82274607, ss84617197, ss88750483, ss110972830, ss115083299, ss168721443, ss170778474, ss175261020, ss203134792, ss207549820, ss255361435, ss281148036, ss286445453, ss291126740, ss1598562898 NC_000011.8:101999953:G:A NC_000011.10:102624012:G:A (self)
55296521, 30687245, 21744112, 2710451, 13697048, 32633354, 11773610, 14303280, 29031675, 7703144, 61589764, 30687245, 6810608, ss225429073, ss235695119, ss242298144, ss562786816, ss658309396, ss988898743, ss1077998038, ss1342723504, ss1426742622, ss1575916062, ss1627331079, ss1670325112, ss1806969957, ss1932261350, ss1967443183, ss2026875008, ss2155186790, ss2627910716, ss2699491501, ss2903770015, ss3008684252, ss3349766709, ss3676005864, ss3738488745, ss3749736696, ss3787050988, ss3792177828, ss3797060326, ss3832808326, ss3839965760, ss3877014695, ss3925455960, ss5203620457, ss5401859571, ss5510496292, ss5651953302, ss5837146233, ss5943275315, ss5980699161 NC_000011.9:102494743:G:A NC_000011.10:102624012:G:A (self)
72595547, 390200921, 27009455, 85828035, 113372743, 8977625746, ss2185198723, ss3027236170, ss3649690755, ss3692482339, ss3815070052, ss3845446951, ss3970631454, ss4897827087, ss5288692138, ss5483701825, ss5585069612, ss5751990931, ss5812726029, ss5850125257, ss5921412628 NC_000011.10:102624012:G:A NC_000011.10:102624012:G:A (self)
ss16123963, ss17428224, ss19206965, ss20843447 NT_033899.6:6038595:G:A NC_000011.10:102624012:G:A (self)
ss3374149, ss3454943, ss28446759, ss38690031, ss97506031, ss106766195, ss132784312, ss137876631, ss156720619 NT_033899.8:6057159:G:A NC_000011.10:102624012:G:A (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 rs2245697

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