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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.

rs3020676

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr10:87333 (GRCh38.p13) 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>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.488050 (129182/264690, TOPMED)
C=0.25406 (4258/16760, 8.3KJPN)
C=0.30758 (3165/10290, ALFA) (+ 13 more)
C=0.4221 (2114/5008, 1000G)
C=0.4779 (1842/3854, ALSPAC)
C=0.4738 (1757/3708, TWINSUK)
C=0.2338 (685/2930, KOREAN)
C=0.2249 (412/1832, Korea1K)
G=0.500 (499/998, GoNL)
C=0.500 (499/998, GoNL)
C=0.417 (250/600, NorthernSweden)
G=0.342 (123/360, SGDP_PRJ)
C=0.464 (140/302, HapMap)
C=0.431 (93/216, Qatari)
G=0.42 (17/40, GENOME_DK)
G=0.42 (15/36, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
None
Publications
0 citations
Genomic View
See rs on genome
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.p13 chr 10 NC_000010.11:g.87333G>A
GRCh38.p13 chr 10 NC_000010.11:g.87333G>C
GRCh37.p13 chr 10 NC_000010.10:g.133273G>A
GRCh37.p13 chr 10 NC_000010.10:g.133273G>C
GRCh37.p13 chr 10 fix patch HG905_PATCH NW_003571043.1:g.77333G>A
GRCh37.p13 chr 10 fix patch HG905_PATCH NW_003571043.1:g.77333G>C
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

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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 10290 G=0.69242 A=0.00000, C=0.30758
European Sub 8810 G=0.6625 A=0.0000, C=0.3375
African Sub 674 G=0.883 A=0.000, C=0.117
African Others Sub 40 G=0.90 A=0.00, C=0.10
African American Sub 634 G=0.882 A=0.000, C=0.118
Asian Sub 72 G=0.97 A=0.00, C=0.03
East Asian Sub 60 G=0.97 A=0.00, C=0.03
Other Asian Sub 12 G=1.00 A=0.00, C=0.00
Latin American 1 Sub 30 G=1.00 A=0.00, C=0.00
Latin American 2 Sub 262 G=1.000 A=0.000, C=0.000
South Asian Sub 50 G=0.96 A=0.00, C=0.04
Other Sub 392 G=0.722 A=0.000, C=0.278


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=0.511950 C=0.488050
8.3KJPN JAPANESE Study-wide 16760 G=0.74594 C=0.25406
1000Genomes Global Study-wide 5008 G=0.5779 C=0.4221
1000Genomes African Sub 1322 G=0.4107 C=0.5893
1000Genomes East Asian Sub 1008 G=0.7718 C=0.2282
1000Genomes Europe Sub 1006 G=0.5288 C=0.4712
1000Genomes South Asian Sub 978 G=0.691 C=0.309
1000Genomes American Sub 694 G=0.526 C=0.474
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.5221 C=0.4779
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.5262 C=0.4738
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.7662 C=0.2338
Korean Genome Project KOREAN Study-wide 1832 G=0.7751 C=0.2249
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.500 C=0.500
Northern Sweden ACPOP Study-wide 600 G=0.583 C=0.417
SGDP_PRJ Global Study-wide 360 G=0.342 C=0.658
HapMap Global Study-wide 302 G=0.536 C=0.464
HapMap American Sub 118 G=0.508 C=0.492
HapMap African Sub 108 G=0.370 C=0.630
HapMap Asian Sub 76 G=0.82 C=0.18
Qatari Global Study-wide 216 G=0.569 C=0.431
The Danish reference pan genome Danish Study-wide 40 G=0.42 C=0.57
Siberian Global Study-wide 36 G=0.42 C=0.58
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 C
GRCh38.p13 chr 10 NC_000010.11:g.87333= NC_000010.11:g.87333G>A NC_000010.11:g.87333G>C
GRCh37.p13 chr 10 NC_000010.10:g.133273= NC_000010.10:g.133273G>A NC_000010.10:g.133273G>C
GRCh37.p13 chr 10 fix patch HG905_PATCH NW_003571043.1:g.77333= NW_003571043.1:g.77333G>A NW_003571043.1:g.77333G>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#.

65 SubSNP, 17 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_JCM ss4249083 Nov 05, 2001 (101)
2 SC_SNP ss12973458 Dec 05, 2003 (119)
3 SC_SNP ss15593685 Feb 27, 2004 (120)
4 SSAHASNP ss20695405 Apr 05, 2004 (121)
5 ABI ss38541022 Mar 15, 2006 (126)
6 HGSV ss78339187 Dec 06, 2007 (129)
7 HGSV ss78955209 Dec 06, 2007 (129)
8 BCMHGSC_JDW ss88057428 Mar 23, 2008 (129)
9 HUMANGENOME_JCVI ss97613055 Feb 06, 2009 (130)
10 ENSEMBL ss107935998 Feb 06, 2009 (130)
11 1000GENOMES ss109145765 Jan 23, 2009 (130)
12 1000GENOMES ss115221535 Jan 25, 2009 (130)
13 ILLUMINA-UK ss118963251 Feb 15, 2009 (130)
14 ENSEMBL ss131849386 Dec 01, 2009 (131)
15 COMPLETE_GENOMICS ss167614011 Jul 04, 2010 (132)
16 COMPLETE_GENOMICS ss168823580 Jul 04, 2010 (132)
17 BUSHMAN ss201023373 Jul 04, 2010 (132)
18 BCM-HGSC-SUB ss207361269 Jul 04, 2010 (132)
19 1000GENOMES ss224512379 Jul 14, 2010 (132)
20 1000GENOMES ss235012276 Jul 15, 2010 (132)
21 1000GENOMES ss241753223 Jul 15, 2010 (132)
22 BL ss253971559 May 09, 2011 (134)
23 GMI ss280440388 May 04, 2012 (137)
24 PJP ss290815797 May 09, 2011 (134)
25 TISHKOFF ss561707930 Apr 25, 2013 (138)
26 SSMP ss656208271 Apr 25, 2013 (138)
27 EVA-GONL ss987096771 Aug 21, 2014 (142)
28 JMKIDD_LAB ss1076687407 Aug 21, 2014 (142)
29 1000GENOMES ss1335912902 Aug 21, 2014 (142)
30 DDI ss1426189103 Apr 09, 2015 (144)
31 EVA_GENOME_DK ss1574842101 Apr 09, 2015 (144)
32 EVA_DECODE ss1596744265 Apr 01, 2015 (144)
33 EVA_UK10K_ALSPAC ss1623797590 Apr 09, 2015 (144)
34 EVA_UK10K_TWINSUK ss1666791623 Apr 09, 2015 (144)
35 HAMMER_LAB ss1806212558 Sep 11, 2015 (146)
36 WEILL_CORNELL_DGM ss1930414753 Feb 17, 2016 (147)
37 GENOMED ss1967034972 Sep 28, 2016 (149)
38 JJLAB ss2025929569 Sep 28, 2016 (149)
39 USC_VALOUEV ss2154169623 Oct 12, 2018 (152)
40 SYSTEMSBIOZJU ss2627432625 Oct 12, 2018 (152)
41 GRF ss2698389019 Oct 12, 2018 (152)
42 GNOMAD ss2884519181 Oct 12, 2018 (152)
43 SWEGEN ss3005784416 Oct 12, 2018 (152)
44 BIOINF_KMB_FNS_UNIBA ss3026746712 Nov 08, 2017 (151)
45 TOPMED ss3109332353 Nov 08, 2017 (151)
46 TOPMED ss3109332354 Nov 08, 2017 (151)
47 CSHL ss3348911615 Oct 12, 2018 (152)
48 URBANLAB ss3649265498 Oct 12, 2018 (152)
49 EVA_DECODE ss3689095342 Jul 13, 2019 (153)
50 ACPOP ss3736974310 Jul 13, 2019 (153)
51 EVA ss3747627344 Jul 13, 2019 (153)
52 PACBIO ss3786553495 Jul 13, 2019 (153)
53 PACBIO ss3791748150 Jul 13, 2019 (153)
54 PACBIO ss3796629772 Jul 13, 2019 (153)
55 KHV_HUMAN_GENOMES ss3812993328 Jul 13, 2019 (153)
56 EVA ss3831916741 Apr 26, 2020 (154)
57 EVA ss3839487151 Apr 26, 2020 (154)
58 EVA ss3844952619 Apr 26, 2020 (154)
59 SGDP_PRJ ss3873326446 Apr 26, 2020 (154)
60 KRGDB ss3921253471 Apr 26, 2020 (154)
61 KOGIC ss3967022857 Apr 26, 2020 (154)
62 GNOMAD ss4211410706 Apr 26, 2021 (155)
63 GNOMAD ss4211410707 Apr 26, 2021 (155)
64 TOPMED ss4839523878 Apr 26, 2021 (155)
65 TOMMO_GENOMICS ss5195848081 Apr 26, 2021 (155)
66 1000Genomes NC_000010.10 - 133273 Oct 12, 2018 (152)
67 The Avon Longitudinal Study of Parents and Children NC_000010.10 - 133273 Oct 12, 2018 (152)
68 The Danish reference pan genome NC_000010.10 - 133273 Apr 26, 2020 (154)
69 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 340933885 (NC_000010.11:87332:G:A 2/139820)
Row 340933886 (NC_000010.11:87332:G:C 68773/139754)

- Apr 26, 2021 (155)
70 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 340933885 (NC_000010.11:87332:G:A 2/139820)
Row 340933886 (NC_000010.11:87332:G:C 68773/139754)

- Apr 26, 2021 (155)
71 Genome of the Netherlands Release 5 NC_000010.10 - 133273 Apr 26, 2020 (154)
72 HapMap NC_000010.11 - 87333 Apr 26, 2020 (154)
73 KOREAN population from KRGDB NC_000010.10 - 133273 Apr 26, 2020 (154)
74 Korean Genome Project NC_000010.11 - 87333 Apr 26, 2020 (154)
75 Northern Sweden NC_000010.10 - 133273 Jul 13, 2019 (153)
76 Qatari NC_000010.10 - 133273 Apr 26, 2020 (154)
77 SGDP_PRJ NC_000010.10 - 133273 Apr 26, 2020 (154)
78 Siberian NC_000010.10 - 133273 Apr 26, 2020 (154)
79 8.3KJPN NC_000010.10 - 133273 Apr 26, 2021 (155)
80 TopMed NC_000010.11 - 87333 Apr 26, 2021 (155)
81 UK 10K study - Twins NC_000010.10 - 133273 Oct 12, 2018 (152)
82 ALFA NC_000010.11 - 87333 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss2884519181 NC_000010.10:133272:G:A NC_000010.11:87332:G:A (self)
13184314281, ss3109332353, ss4211410706 NC_000010.11:87332:G:A NC_000010.11:87332:G:A (self)
ss78339187, ss78955209 NC_000010.8:123272:G:C NC_000010.11:87332:G:C (self)
ss88057428, ss109145765, ss115221535, ss118963251, ss167614011, ss168823580, ss201023373, ss207361269, ss253971559, ss280440388, ss290815797, ss1596744265 NC_000010.9:123272:G:C NC_000010.11:87332:G:C (self)
48246610, 26806373, 1988114, 11953898, 28430865, 10259175, 12456683, 25343426, 6685977, 53817388, 26806373, ss224512379, ss235012276, ss241753223, ss561707930, ss656208271, ss987096771, ss1076687407, ss1335912902, ss1426189103, ss1574842101, ss1623797590, ss1666791623, ss1806212558, ss1930414753, ss1967034972, ss2025929569, ss2154169623, ss2627432625, ss2698389019, ss2884519181, ss3005784416, ss3348911615, ss3736974310, ss3747627344, ss3786553495, ss3791748150, ss3796629772, ss3831916741, ss3839487151, ss3873326446, ss3921253471, ss5195848081 NC_000010.10:133272:G:C NC_000010.11:87332:G:C (self)
317103, 23400858, 34602486, 55069533, 13184314281, ss3026746712, ss3109332354, ss3649265498, ss3689095342, ss3812993328, ss3844952619, ss3967022857, ss4211410707, ss4839523878 NC_000010.11:87332:G:C NC_000010.11:87332:G:C (self)
ss4249083, ss38541022, ss97613055, ss107935998, ss131849386 NT_008705.16:73272:G:C NC_000010.11:87332:G:C (self)
ss12973458 NT_024115.14:73272:G:C NC_000010.11:87332:G:C (self)
ss15593685, ss20695405 NT_077567.3:73272:G:C NC_000010.11:87332:G:C (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 rs3020676

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.post596+ae089ad