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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.

rs9977951

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr21:40841029 (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 / G>T
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.081473 (21565/264690, TOPMED)
A=0.05912 (1896/32068, ALFA)
A=0.20943 (5918/28258, 14KJPN) (+ 17 more)
A=0.20937 (3509/16760, 8.3KJPN)
A=0.0904 (579/6404, 1000G_30x)
A=0.0909 (455/5008, 1000G)
A=0.0942 (422/4480, Estonian)
A=0.0885 (341/3854, ALSPAC)
A=0.0885 (328/3708, TWINSUK)
A=0.1345 (394/2930, KOREAN)
A=0.1348 (247/1832, Korea1K)
A=0.0591 (66/1116, Daghestan)
A=0.084 (84/998, GoNL)
A=0.088 (53/600, NorthernSweden)
A=0.111 (24/216, Qatari)
A=0.120 (26/216, Vietnamese)
G=0.484 (59/122, SGDP_PRJ)
A=0.15 (10/66, Ancient Sardinia)
A=0.12 (5/40, GENOME_DK)
G=0.4 (4/10, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
DSCAM : 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 32068 G=0.94088 A=0.05912, T=0.00000
European Sub 23718 G=0.93275 A=0.06725, T=0.00000
African Sub 5592 G=0.9689 A=0.0311, T=0.0000
African Others Sub 200 G=0.985 A=0.015, T=0.000
African American Sub 5392 G=0.9683 A=0.0317, T=0.0000
Asian Sub 102 G=0.961 A=0.039, T=0.000
East Asian Sub 84 G=0.96 A=0.04, T=0.00
Other Asian Sub 18 G=0.94 A=0.06, T=0.00
Latin American 1 Sub 144 G=0.979 A=0.021, T=0.000
Latin American 2 Sub 546 G=0.974 A=0.026, T=0.000
South Asian Sub 100 G=0.98 A=0.02, T=0.00
Other Sub 1866 G=0.9443 A=0.0557, T=0.0000


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=0.918527 A=0.081473
Allele Frequency Aggregator Total Global 32068 G=0.94088 A=0.05912, T=0.00000
Allele Frequency Aggregator European Sub 23718 G=0.93275 A=0.06725, T=0.00000
Allele Frequency Aggregator African Sub 5592 G=0.9689 A=0.0311, T=0.0000
Allele Frequency Aggregator Other Sub 1866 G=0.9443 A=0.0557, T=0.0000
Allele Frequency Aggregator Latin American 2 Sub 546 G=0.974 A=0.026, T=0.000
Allele Frequency Aggregator Latin American 1 Sub 144 G=0.979 A=0.021, T=0.000
Allele Frequency Aggregator Asian Sub 102 G=0.961 A=0.039, T=0.000
Allele Frequency Aggregator South Asian Sub 100 G=0.98 A=0.02, T=0.00
14KJPN JAPANESE Study-wide 28258 G=0.79057 A=0.20943
8.3KJPN JAPANESE Study-wide 16760 G=0.79063 A=0.20937
1000Genomes_30x Global Study-wide 6404 G=0.9096 A=0.0904
1000Genomes_30x African Sub 1786 G=0.9552 A=0.0448
1000Genomes_30x Europe Sub 1266 G=0.9123 A=0.0877
1000Genomes_30x South Asian Sub 1202 G=0.8927 A=0.1073
1000Genomes_30x East Asian Sub 1170 G=0.8897 A=0.1103
1000Genomes_30x American Sub 980 G=0.867 A=0.133
1000Genomes Global Study-wide 5008 G=0.9091 A=0.0909
1000Genomes African Sub 1322 G=0.9584 A=0.0416
1000Genomes East Asian Sub 1008 G=0.8889 A=0.1111
1000Genomes Europe Sub 1006 G=0.9125 A=0.0875
1000Genomes South Asian Sub 978 G=0.887 A=0.113
1000Genomes American Sub 694 G=0.872 A=0.128
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.9058 A=0.0942
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.9115 A=0.0885
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.9115 A=0.0885
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.8655 A=0.1345
Korean Genome Project KOREAN Study-wide 1832 G=0.8652 A=0.1348
Genome-wide autozygosity in Daghestan Global Study-wide 1116 G=0.9409 A=0.0591
Genome-wide autozygosity in Daghestan Daghestan Sub 628 G=0.951 A=0.049
Genome-wide autozygosity in Daghestan Near_East Sub 134 G=0.933 A=0.067
Genome-wide autozygosity in Daghestan Central Asia Sub 122 G=0.910 A=0.090
Genome-wide autozygosity in Daghestan Europe Sub 108 G=0.935 A=0.065
Genome-wide autozygosity in Daghestan South Asian Sub 88 G=0.93 A=0.07
Genome-wide autozygosity in Daghestan Caucasus Sub 36 G=0.94 A=0.06
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.916 A=0.084
Northern Sweden ACPOP Study-wide 600 G=0.912 A=0.088
Qatari Global Study-wide 216 G=0.889 A=0.111
A Vietnamese Genetic Variation Database Global Study-wide 216 G=0.880 A=0.120
SGDP_PRJ Global Study-wide 122 G=0.484 A=0.516
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 66 G=0.85 A=0.15
The Danish reference pan genome Danish Study-wide 40 G=0.88 A=0.12
Siberian Global Study-wide 10 G=0.4 A=0.6
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 21 NC_000021.9:g.40841029G>A
GRCh38.p14 chr 21 NC_000021.9:g.40841029G>T
GRCh37.p13 chr 21 NC_000021.8:g.42212955G>A
GRCh37.p13 chr 21 NC_000021.8:g.42212955G>T
GRCh38.p14 chr 21 fix patch HG2265_PATCH NW_025791814.1:g.980683G>A
GRCh38.p14 chr 21 fix patch HG2265_PATCH NW_025791814.1:g.980683G>T
Gene: DSCAM, DS cell adhesion molecule (minus strand)
Molecule type Change Amino acid[Codon] SO Term
DSCAM transcript variant 2 NM_001271534.3:c.43+5590C…

NM_001271534.3:c.43+5590C>T

 		N/A Intron Variant
DSCAM transcript variant 1 NM_001389.5:c.43+5590C>T N/A Intron Variant
DSCAM transcript variant 3 NR_073202.3:n. N/A Intron Variant
DSCAM transcript variant X1 XM_017028281.2:c. 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 T
GRCh38.p14 chr 21 NC_000021.9:g.40841029= NC_000021.9:g.40841029G>A NC_000021.9:g.40841029G>T
GRCh37.p13 chr 21 NC_000021.8:g.42212955= NC_000021.8:g.42212955G>A NC_000021.8:g.42212955G>T
GRCh38.p14 chr 21 fix patch HG2265_PATCH NW_025791814.1:g.980683= NW_025791814.1:g.980683G>A NW_025791814.1:g.980683G>T
DSCAM transcript variant 2 NM_001271534.1:c.43+5590= NM_001271534.1:c.43+5590C>T NM_001271534.1:c.43+5590C>A
DSCAM transcript variant 2 NM_001271534.3:c.43+5590= NM_001271534.3:c.43+5590C>T NM_001271534.3:c.43+5590C>A
DSCAM transcript variant 1 NM_001389.3:c.43+5590= NM_001389.3:c.43+5590C>T NM_001389.3:c.43+5590C>A
DSCAM transcript variant 1 NM_001389.5:c.43+5590= NM_001389.5:c.43+5590C>T NM_001389.5:c.43+5590C>A
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#.

64 SubSNP, 22 Frequency submissions
No Submitter Submission ID Date (Build)
1 WUGSC_SSAHASNP ss13820421 Dec 05, 2003 (119)
2 1000GENOMES ss228577944 Jul 14, 2010 (132)
3 1000GENOMES ss237991847 Jul 15, 2010 (132)
4 1000GENOMES ss244128902 Jul 15, 2010 (132)
5 BL ss255977955 May 09, 2011 (134)
6 GMI ss283551278 May 04, 2012 (137)
7 ILLUMINA ss483377588 May 04, 2012 (137)
8 ILLUMINA ss484273981 May 04, 2012 (137)
9 ILLUMINA ss535590503 Sep 08, 2015 (146)
10 TISHKOFF ss566511535 Apr 25, 2013 (138)
11 SSMP ss662422311 Apr 25, 2013 (138)
12 ILLUMINA ss780254584 Sep 08, 2015 (146)
13 ILLUMINA ss782131932 Sep 08, 2015 (146)
14 ILLUMINA ss835740310 Sep 08, 2015 (146)
15 EVA-GONL ss995143335 Aug 21, 2014 (142)
16 JMKIDD_LAB ss1082518884 Aug 21, 2014 (142)
17 1000GENOMES ss1366381899 Aug 21, 2014 (142)
18 HAMMER_LAB ss1397781137 Sep 08, 2015 (146)
19 DDI ss1429192002 Apr 01, 2015 (144)
20 EVA_GENOME_DK ss1579673062 Apr 01, 2015 (144)
21 EVA_UK10K_ALSPAC ss1639612793 Apr 01, 2015 (144)
22 EVA_UK10K_TWINSUK ss1682606826 Apr 01, 2015 (144)
23 EVA_DECODE ss1699215015 Apr 01, 2015 (144)
24 WEILL_CORNELL_DGM ss1938693532 Feb 12, 2016 (147)
25 GENOMED ss1969231446 Jul 19, 2016 (147)
26 JJLAB ss2030120108 Sep 14, 2016 (149)
27 USC_VALOUEV ss2158725116 Dec 20, 2016 (150)
28 HUMAN_LONGEVITY ss2245968329 Dec 20, 2016 (150)
29 ILLUMINA ss2633852194 Nov 08, 2017 (151)
30 GRF ss2704456829 Nov 08, 2017 (151)
31 GNOMAD ss2972056766 Nov 08, 2017 (151)
32 AFFY ss2985848934 Nov 08, 2017 (151)
33 SWEGEN ss3018931255 Nov 08, 2017 (151)
34 BIOINF_KMB_FNS_UNIBA ss3028899592 Nov 08, 2017 (151)
35 CSHL ss3352730440 Nov 08, 2017 (151)
36 ILLUMINA ss3628486796 Oct 12, 2018 (152)
37 ILLUMINA ss3631805577 Oct 12, 2018 (152)
38 ILLUMINA ss3642206091 Oct 12, 2018 (152)
39 EGCUT_WGS ss3685508674 Jul 13, 2019 (153)
40 EVA_DECODE ss3707780581 Jul 13, 2019 (153)
41 ACPOP ss3743753845 Jul 13, 2019 (153)
42 EVA ss3759137244 Jul 13, 2019 (153)
43 KHV_HUMAN_GENOMES ss3822304214 Jul 13, 2019 (153)
44 EVA ss3835887613 Apr 27, 2020 (154)
45 EVA ss3841571332 Apr 27, 2020 (154)
46 EVA ss3847084921 Apr 27, 2020 (154)
47 SGDP_PRJ ss3890053178 Apr 27, 2020 (154)
48 KRGDB ss3940398601 Apr 27, 2020 (154)
49 KOGIC ss3983140860 Apr 27, 2020 (154)
50 EVA ss3985905539 Apr 27, 2021 (155)
51 TOPMED ss5102430985 Apr 27, 2021 (155)
52 TOMMO_GENOMICS ss5231638320 Apr 27, 2021 (155)
53 1000G_HIGH_COVERAGE ss5310302005 Oct 13, 2022 (156)
54 EVA ss5316040310 Oct 13, 2022 (156)
55 EVA ss5440040647 Oct 13, 2022 (156)
56 HUGCELL_USP ss5502342188 Oct 13, 2022 (156)
57 1000G_HIGH_COVERAGE ss5617483433 Oct 13, 2022 (156)
58 SANFORD_IMAGENETICS ss5664062769 Oct 13, 2022 (156)
59 TOMMO_GENOMICS ss5792180737 Oct 13, 2022 (156)
60 YY_MCH ss5818465485 Oct 13, 2022 (156)
61 EVA ss5839074361 Oct 13, 2022 (156)
62 EVA ss5853316612 Oct 13, 2022 (156)
63 EVA ss5892453473 Oct 13, 2022 (156)
64 EVA ss5958960596 Oct 13, 2022 (156)
65 1000Genomes NC_000021.8 - 42212955 Oct 12, 2018 (152)
66 1000Genomes_30x NC_000021.9 - 40841029 Oct 13, 2022 (156)
67 The Avon Longitudinal Study of Parents and Children NC_000021.8 - 42212955 Oct 12, 2018 (152)
68 Genome-wide autozygosity in Daghestan NC_000021.7 - 41134825 Apr 27, 2020 (154)
69 Genetic variation in the Estonian population NC_000021.8 - 42212955 Oct 12, 2018 (152)
70 The Danish reference pan genome NC_000021.8 - 42212955 Apr 27, 2020 (154)
71 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 563854802 (NC_000021.9:40841028:G:A 11284/140198)
Row 563854803 (NC_000021.9:40841028:G:T 1/140218)

- Apr 27, 2021 (155)
72 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 563854802 (NC_000021.9:40841028:G:A 11284/140198)
Row 563854803 (NC_000021.9:40841028:G:T 1/140218)

- Apr 27, 2021 (155)
73 Genome of the Netherlands Release 5 NC_000021.8 - 42212955 Apr 27, 2020 (154)
74 KOREAN population from KRGDB NC_000021.8 - 42212955 Apr 27, 2020 (154)
75 Korean Genome Project NC_000021.9 - 40841029 Apr 27, 2020 (154)
76 Northern Sweden NC_000021.8 - 42212955 Jul 13, 2019 (153)
77 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000021.8 - 42212955 Apr 27, 2021 (155)
78 Qatari NC_000021.8 - 42212955 Apr 27, 2020 (154)
79 SGDP_PRJ NC_000021.8 - 42212955 Apr 27, 2020 (154)
80 Siberian NC_000021.8 - 42212955 Apr 27, 2020 (154)
81 8.3KJPN NC_000021.8 - 42212955 Apr 27, 2021 (155)
82 14KJPN NC_000021.9 - 40841029 Oct 13, 2022 (156)
83 TopMed NC_000021.9 - 40841029 Apr 27, 2021 (155)
84 UK 10K study - Twins NC_000021.8 - 42212955 Oct 12, 2018 (152)
85 A Vietnamese Genetic Variation Database NC_000021.8 - 42212955 Jul 13, 2019 (153)
86 ALFA NC_000021.9 - 40841029 Apr 27, 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
295142, ss255977955, ss283551278, ss484273981, ss1397781137, ss1699215015 NC_000021.7:41134824:G:A NC_000021.9:40841028:G:A (self)
79905564, 44225896, 31246922, 5838001, 19700598, 47575995, 17038710, 1131466, 20735454, 42070158, 11241470, 89607627, 44225896, 9758781, ss228577944, ss237991847, ss244128902, ss483377588, ss535590503, ss566511535, ss662422311, ss780254584, ss782131932, ss835740310, ss995143335, ss1082518884, ss1366381899, ss1429192002, ss1579673062, ss1639612793, ss1682606826, ss1938693532, ss1969231446, ss2030120108, ss2158725116, ss2633852194, ss2704456829, ss2972056766, ss2985848934, ss3018931255, ss3352730440, ss3628486796, ss3631805577, ss3642206091, ss3685508674, ss3743753845, ss3759137244, ss3835887613, ss3841571332, ss3890053178, ss3940398601, ss3985905539, ss5231638320, ss5316040310, ss5440040647, ss5664062769, ss5839074361, ss5958960596 NC_000021.8:42212954:G:A NC_000021.9:40841028:G:A (self)
105009368, 39518861, 126017841, 377539931, 2051085790, ss2245968329, ss3028899592, ss3707780581, ss3822304214, ss3847084921, ss3983140860, ss5102430985, ss5310302005, ss5502342188, ss5617483433, ss5792180737, ss5818465485, ss5853316612, ss5892453473 NC_000021.9:40841028:G:A NC_000021.9:40841028:G:A (self)
ss13820421 NT_011512.9:27873350:G:A NC_000021.9:40841028:G:A (self)
2051085790 NC_000021.9:40841028:G:T NC_000021.9:40841028:G:T (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 rs9977951

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