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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.

rs478327

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:33748893 (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
T>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.083513 (22105/264690, TOPMED)
G=0.080431 (11268/140096, GnomAD)
G=0.06416 (1813/28258, 14KJPN) (+ 18 more)
G=0.08168 (1543/18890, ALFA)
G=0.06480 (1086/16760, 8.3KJPN)
G=0.0837 (536/6404, 1000G_30x)
G=0.0809 (405/5008, 1000G)
G=0.0857 (384/4480, Estonian)
G=0.0747 (288/3854, ALSPAC)
G=0.0707 (262/3708, TWINSUK)
G=0.0465 (136/2922, KOREAN)
G=0.0469 (86/1832, Korea1K)
G=0.073 (73/998, GoNL)
G=0.098 (59/600, NorthernSweden)
G=0.037 (8/216, Qatari)
G=0.019 (4/216, Vietnamese)
G=0.05 (4/88, HapMap)
T=0.47 (28/60, SGDP_PRJ)
G=0.03 (1/40, GENOME_DK)
T=0.50 (6/12, Siberian)
G=0.50 (6/12, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
CSMD2 : 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 T=0.91832 G=0.08168
European Sub 14286 T=0.92601 G=0.07399
African Sub 2946 T=0.8958 G=0.1042
African Others Sub 114 T=0.895 G=0.105
African American Sub 2832 T=0.8958 G=0.1042
Asian Sub 112 T=0.938 G=0.062
East Asian Sub 86 T=0.93 G=0.07
Other Asian Sub 26 T=0.96 G=0.04
Latin American 1 Sub 146 T=0.884 G=0.116
Latin American 2 Sub 610 T=0.866 G=0.134
South Asian Sub 98 T=0.91 G=0.09
Other Sub 692 T=0.908 G=0.092


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 T=0.916487 G=0.083513
gnomAD - Genomes Global Study-wide 140096 T=0.919569 G=0.080431
gnomAD - Genomes European Sub 75874 T=0.92946 G=0.07054
gnomAD - Genomes African Sub 41982 T=0.90722 G=0.09278
gnomAD - Genomes American Sub 13636 T=0.88780 G=0.11220
gnomAD - Genomes Ashkenazi Jewish Sub 3324 T=0.9480 G=0.0520
gnomAD - Genomes East Asian Sub 3128 T=0.9546 G=0.0454
gnomAD - Genomes Other Sub 2152 T=0.9182 G=0.0818
14KJPN JAPANESE Study-wide 28258 T=0.93584 G=0.06416
Allele Frequency Aggregator Total Global 18890 T=0.91832 G=0.08168
Allele Frequency Aggregator European Sub 14286 T=0.92601 G=0.07399
Allele Frequency Aggregator African Sub 2946 T=0.8958 G=0.1042
Allele Frequency Aggregator Other Sub 692 T=0.908 G=0.092
Allele Frequency Aggregator Latin American 2 Sub 610 T=0.866 G=0.134
Allele Frequency Aggregator Latin American 1 Sub 146 T=0.884 G=0.116
Allele Frequency Aggregator Asian Sub 112 T=0.938 G=0.062
Allele Frequency Aggregator South Asian Sub 98 T=0.91 G=0.09
8.3KJPN JAPANESE Study-wide 16760 T=0.93520 G=0.06480
1000Genomes_30x Global Study-wide 6404 T=0.9163 G=0.0837
1000Genomes_30x African Sub 1786 T=0.9043 G=0.0957
1000Genomes_30x Europe Sub 1266 T=0.9344 G=0.0656
1000Genomes_30x South Asian Sub 1202 T=0.9210 G=0.0790
1000Genomes_30x East Asian Sub 1170 T=0.9701 G=0.0299
1000Genomes_30x American Sub 980 T=0.845 G=0.155
1000Genomes Global Study-wide 5008 T=0.9191 G=0.0809
1000Genomes African Sub 1322 T=0.9107 G=0.0893
1000Genomes East Asian Sub 1008 T=0.9692 G=0.0308
1000Genomes Europe Sub 1006 T=0.9364 G=0.0636
1000Genomes South Asian Sub 978 T=0.916 G=0.084
1000Genomes American Sub 694 T=0.841 G=0.159
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.9143 G=0.0857
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.9253 G=0.0747
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.9293 G=0.0707
KOREAN population from KRGDB KOREAN Study-wide 2922 T=0.9535 G=0.0465
Korean Genome Project KOREAN Study-wide 1832 T=0.9531 G=0.0469
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.927 G=0.073
Northern Sweden ACPOP Study-wide 600 T=0.902 G=0.098
Qatari Global Study-wide 216 T=0.963 G=0.037
A Vietnamese Genetic Variation Database Global Study-wide 216 T=0.981 G=0.019
HapMap Global Study-wide 88 T=0.95 G=0.05
HapMap Asian Sub 88 T=0.95 G=0.05
SGDP_PRJ Global Study-wide 60 T=0.47 G=0.53
The Danish reference pan genome Danish Study-wide 40 T=0.97 G=0.03
Siberian Global Study-wide 12 T=0.50 G=0.50
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.33748893T>G
GRCh37.p13 chr 1 NC_000001.10:g.34214494T>G
CSMD2 RefSeqGene NG_053181.1:g.421950A>C
Gene: CSMD2, CUB and Sushi multiple domains 2 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
CSMD2 transcript variant 1 NM_001281956.2:c.1847-528…

NM_001281956.2:c.1847-5287A>C

 		N/A Intron Variant
CSMD2 transcript variant 2 NM_052896.5:c.1727-5287A>C N/A Intron Variant
CSMD2 transcript variant X2 XM_017000185.2:c.1847-528…

XM_017000185.2:c.1847-5287A>C

 		N/A Intron Variant
CSMD2 transcript variant X7 XM_017000191.2:c.1847-528…

XM_017000191.2:c.1847-5287A>C

 		N/A Intron Variant
CSMD2 transcript variant X8 XM_017000192.2:c.1847-528…

XM_017000192.2:c.1847-5287A>C

 		N/A Intron Variant
CSMD2 transcript variant X9 XM_017000193.2:c.1847-528…

XM_017000193.2:c.1847-5287A>C

 		N/A Intron Variant
CSMD2 transcript variant X1 XM_047443607.1:c.1847-528…

XM_047443607.1:c.1847-5287A>C

 		N/A Intron Variant
CSMD2 transcript variant X3 XM_047443642.1:c.1847-528…

XM_047443642.1:c.1847-5287A>C

 		N/A Intron Variant
CSMD2 transcript variant X4 XM_047443656.1:c.1727-528…

XM_047443656.1:c.1727-5287A>C

 		N/A Intron Variant
CSMD2 transcript variant X5 XM_047443661.1:c.1847-528…

XM_047443661.1:c.1847-5287A>C

 		N/A Intron Variant
CSMD2 transcript variant X6 XM_047443666.1:c.1112-528…

XM_047443666.1:c.1112-5287A>C

 		N/A Intron Variant
CSMD2 transcript variant X10 XM_047443685.1:c.1727-528…

XM_047443685.1:c.1727-5287A>C

 		N/A Intron 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 T= G
GRCh38.p14 chr 1 NC_000001.11:g.33748893= NC_000001.11:g.33748893T>G
GRCh37.p13 chr 1 NC_000001.10:g.34214494= NC_000001.10:g.34214494T>G
CSMD2 RefSeqGene NG_053181.1:g.421950= NG_053181.1:g.421950A>C
CSMD2 transcript variant 1 NM_001281956.2:c.1847-5287= NM_001281956.2:c.1847-5287A>C
CSMD2 transcript NM_052896.3:c.1727-5287= NM_052896.3:c.1727-5287A>C
CSMD2 transcript variant 2 NM_052896.5:c.1727-5287= NM_052896.5:c.1727-5287A>C
CSMD2 transcript variant X1 XM_005270417.1:c.1847-5287= XM_005270417.1:c.1847-5287A>C
CSMD2 transcript variant X2 XM_017000185.2:c.1847-5287= XM_017000185.2:c.1847-5287A>C
CSMD2 transcript variant X7 XM_017000191.2:c.1847-5287= XM_017000191.2:c.1847-5287A>C
CSMD2 transcript variant X8 XM_017000192.2:c.1847-5287= XM_017000192.2:c.1847-5287A>C
CSMD2 transcript variant X9 XM_017000193.2:c.1847-5287= XM_017000193.2:c.1847-5287A>C
CSMD2 transcript variant X1 XM_047443607.1:c.1847-5287= XM_047443607.1:c.1847-5287A>C
CSMD2 transcript variant X3 XM_047443642.1:c.1847-5287= XM_047443642.1:c.1847-5287A>C
CSMD2 transcript variant X4 XM_047443656.1:c.1727-5287= XM_047443656.1:c.1727-5287A>C
CSMD2 transcript variant X5 XM_047443661.1:c.1847-5287= XM_047443661.1:c.1847-5287A>C
CSMD2 transcript variant X6 XM_047443666.1:c.1112-5287= XM_047443666.1:c.1112-5287A>C
CSMD2 transcript variant X10 XM_047443685.1:c.1727-5287= XM_047443685.1:c.1727-5287A>C
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#.

61 SubSNP, 20 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_JCM ss647834 Aug 11, 2000 (83)
2 KWOK ss873946 Oct 04, 2000 (86)
3 KWOK ss1598278 Oct 18, 2000 (87)
4 TSC-CSHL ss2095380 Oct 23, 2000 (92)
5 TSC-CSHL ss5519332 Oct 08, 2002 (108)
6 SC_JCM ss5859183 Feb 20, 2003 (111)
7 ABI ss41134677 Mar 13, 2006 (126)
8 HUMANGENOME_JCVI ss99199028 Feb 05, 2009 (130)
9 BGI ss102732821 Dec 01, 2009 (131)
10 ENSEMBL ss143669473 Dec 01, 2009 (131)
11 BUSHMAN ss198272844 Jul 04, 2010 (132)
12 1000GENOMES ss218316852 Jul 14, 2010 (132)
13 1000GENOMES ss230485731 Jul 14, 2010 (132)
14 PJP ss290802652 May 09, 2011 (134)
15 TISHKOFF ss553963432 Apr 25, 2013 (138)
16 SSMP ss647728782 Apr 25, 2013 (138)
17 EVA-GONL ss975018182 Aug 21, 2014 (142)
18 JMKIDD_LAB ss1067783428 Aug 21, 2014 (142)
19 1000GENOMES ss1290321032 Aug 21, 2014 (142)
20 EVA_GENOME_DK ss1573979134 Apr 01, 2015 (144)
21 EVA_DECODE ss1584377966 Apr 01, 2015 (144)
22 EVA_UK10K_ALSPAC ss1599874467 Apr 01, 2015 (144)
23 EVA_UK10K_TWINSUK ss1642868500 Apr 01, 2015 (144)
24 HAMMER_LAB ss1794156388 Sep 08, 2015 (146)
25 WEILL_CORNELL_DGM ss1918229616 Feb 12, 2016 (147)
26 JJLAB ss2019625735 Sep 14, 2016 (149)
27 USC_VALOUEV ss2147636148 Dec 20, 2016 (150)
28 HUMAN_LONGEVITY ss2161316003 Dec 20, 2016 (150)
29 GRF ss2697543513 Nov 08, 2017 (151)
30 GNOMAD ss2753504761 Nov 08, 2017 (151)
31 SWEGEN ss2986584791 Nov 08, 2017 (151)
32 CSHL ss3343396115 Nov 08, 2017 (151)
33 BIOINF_KMB_FNS_UNIBA ss3645035537 Oct 11, 2018 (152)
34 URBANLAB ss3646637026 Oct 11, 2018 (152)
35 EGCUT_WGS ss3654647808 Jul 12, 2019 (153)
36 EVA_DECODE ss3686490300 Jul 12, 2019 (153)
37 ACPOP ss3726927420 Jul 12, 2019 (153)
38 EVA ss3746026397 Jul 12, 2019 (153)
39 PACBIO ss3783372806 Jul 12, 2019 (153)
40 PACBIO ss3789038270 Jul 12, 2019 (153)
41 PACBIO ss3793910895 Jul 12, 2019 (153)
42 KHV_HUMAN_GENOMES ss3799043729 Jul 12, 2019 (153)
43 EVA ss3826105017 Apr 25, 2020 (154)
44 EVA ss3836440461 Apr 25, 2020 (154)
45 EVA ss3841845711 Apr 25, 2020 (154)
46 SGDP_PRJ ss3848557246 Apr 25, 2020 (154)
47 KRGDB ss3893507853 Apr 25, 2020 (154)
48 KOGIC ss3944201292 Apr 25, 2020 (154)
49 TOPMED ss4444646881 Apr 25, 2021 (155)
50 TOMMO_GENOMICS ss5143277912 Apr 25, 2021 (155)
51 1000G_HIGH_COVERAGE ss5241767672 Oct 17, 2022 (156)
52 HUGCELL_USP ss5442888286 Oct 17, 2022 (156)
53 EVA ss5505808624 Oct 17, 2022 (156)
54 1000G_HIGH_COVERAGE ss5513796844 Oct 17, 2022 (156)
55 SANFORD_IMAGENETICS ss5625252065 Oct 17, 2022 (156)
56 TOMMO_GENOMICS ss5667835442 Oct 17, 2022 (156)
57 YY_MCH ss5800472892 Oct 17, 2022 (156)
58 EVA ss5831768784 Oct 17, 2022 (156)
59 EVA ss5848850249 Oct 17, 2022 (156)
60 EVA ss5907684500 Oct 17, 2022 (156)
61 EVA ss5937070423 Oct 17, 2022 (156)
62 1000Genomes NC_000001.10 - 34214494 Oct 11, 2018 (152)
63 1000Genomes_30x NC_000001.11 - 33748893 Oct 17, 2022 (156)
64 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 34214494 Oct 11, 2018 (152)
65 Genetic variation in the Estonian population NC_000001.10 - 34214494 Oct 11, 2018 (152)
66 The Danish reference pan genome NC_000001.10 - 34214494 Apr 25, 2020 (154)
67 gnomAD - Genomes NC_000001.11 - 33748893 Apr 25, 2021 (155)
68 Genome of the Netherlands Release 5 NC_000001.10 - 34214494 Apr 25, 2020 (154)
69 HapMap NC_000001.11 - 33748893 Apr 25, 2020 (154)
70 KOREAN population from KRGDB NC_000001.10 - 34214494 Apr 25, 2020 (154)
71 Korean Genome Project NC_000001.11 - 33748893 Apr 25, 2020 (154)
72 Northern Sweden NC_000001.10 - 34214494 Jul 12, 2019 (153)
73 Qatari NC_000001.10 - 34214494 Apr 25, 2020 (154)
74 SGDP_PRJ NC_000001.10 - 34214494 Apr 25, 2020 (154)
75 Siberian NC_000001.10 - 34214494 Apr 25, 2020 (154)
76 8.3KJPN NC_000001.10 - 34214494 Apr 25, 2021 (155)
77 14KJPN NC_000001.11 - 33748893 Oct 17, 2022 (156)
78 TopMed NC_000001.11 - 33748893 Apr 25, 2021 (155)
79 UK 10K study - Twins NC_000001.10 - 34214494 Oct 11, 2018 (152)
80 A Vietnamese Genetic Variation Database NC_000001.10 - 34214494 Jul 12, 2019 (153)
81 ALFA NC_000001.11 - 33748893 Apr 25, 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)
rs1325249 Jan 18, 2001 (92)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss198272844, ss290802652, ss1584377966 NC_000001.9:33987080:T:G NC_000001.11:33748892:T:G (self)
1019205, 546807, 386056, 1450562, 234711, 685247, 212285, 271546, 574226, 152502, 1247219, 546807, 112274, ss218316852, ss230485731, ss553963432, ss647728782, ss975018182, ss1067783428, ss1290321032, ss1573979134, ss1599874467, ss1642868500, ss1794156388, ss1918229616, ss2019625735, ss2147636148, ss2697543513, ss2753504761, ss2986584791, ss3343396115, ss3654647808, ss3726927420, ss3746026397, ss3783372806, ss3789038270, ss3793910895, ss3826105017, ss3836440461, ss3848557246, ss3893507853, ss5143277912, ss5505808624, ss5625252065, ss5831768784, ss5937070423 NC_000001.10:34214493:T:G NC_000001.11:33748892:T:G (self)
1322779, 7182287, 42538, 579293, 1672546, 8253216, 8063666020, ss2161316003, ss3645035537, ss3646637026, ss3686490300, ss3799043729, ss3841845711, ss3944201292, ss4444646881, ss5241767672, ss5442888286, ss5513796844, ss5667835442, ss5800472892, ss5848850249, ss5907684500 NC_000001.11:33748892:T:G NC_000001.11:33748892:T:G (self)
ss647834, ss873946, ss1598278, ss2095380, ss5519332, ss5859183, ss41134677, ss99199028, ss102732821, ss143669473 NT_032977.9:4186411:T:G NC_000001.11:33748892:T:G (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 rs478327

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