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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.

rs2420641

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr10:119650514 (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
A=0.321958 (85219/264690, TOPMED)
A=0.309136 (46175/149368, ALFA)
A=0.323154 (45239/139992, GnomAD) (+ 17 more)
A=0.43920 (12411/28258, 14KJPN)
A=0.44033 (7380/16760, 8.3KJPN)
A=0.3281 (2101/6404, 1000G_30x)
A=0.3289 (1647/5008, 1000G)
A=0.3248 (1455/4480, Estonian)
A=0.2929 (1129/3854, ALSPAC)
A=0.3161 (1172/3708, TWINSUK)
A=0.4082 (1196/2930, KOREAN)
A=0.3550 (671/1890, HapMap)
A=0.4105 (752/1832, Korea1K)
A=0.295 (294/998, GoNL)
A=0.322 (193/600, NorthernSweden)
G=0.388 (114/294, SGDP_PRJ)
A=0.287 (62/216, Qatari)
G=0.486 (104/214, Vietnamese)
A=0.28 (11/40, GENOME_DK)
G=0.38 (13/34, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
BAG3 : 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 149368 G=0.690864 A=0.309136
European Sub 128572 G=0.692592 A=0.307408
African Sub 6676 G=0.6636 A=0.3364
African Others Sub 242 G=0.616 A=0.384
African American Sub 6434 G=0.6654 A=0.3346
Asian Sub 630 G=0.517 A=0.483
East Asian Sub 498 G=0.536 A=0.464
Other Asian Sub 132 G=0.447 A=0.553
Latin American 1 Sub 752 G=0.698 A=0.302
Latin American 2 Sub 6318 G=0.7042 A=0.2958
South Asian Sub 184 G=0.815 A=0.185
Other Sub 6236 G=0.6839 A=0.3161


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=0.678042 A=0.321958
Allele Frequency Aggregator Total Global 149368 G=0.690864 A=0.309136
Allele Frequency Aggregator European Sub 128572 G=0.692592 A=0.307408
Allele Frequency Aggregator African Sub 6676 G=0.6636 A=0.3364
Allele Frequency Aggregator Latin American 2 Sub 6318 G=0.7042 A=0.2958
Allele Frequency Aggregator Other Sub 6236 G=0.6839 A=0.3161
Allele Frequency Aggregator Latin American 1 Sub 752 G=0.698 A=0.302
Allele Frequency Aggregator Asian Sub 630 G=0.517 A=0.483
Allele Frequency Aggregator South Asian Sub 184 G=0.815 A=0.185
gnomAD - Genomes Global Study-wide 139992 G=0.676846 A=0.323154
gnomAD - Genomes European Sub 75852 G=0.69111 A=0.30889
gnomAD - Genomes African Sub 41892 G=0.65487 A=0.34513
gnomAD - Genomes American Sub 13648 G=0.70179 A=0.29821
gnomAD - Genomes Ashkenazi Jewish Sub 3324 G=0.6998 A=0.3002
gnomAD - Genomes East Asian Sub 3130 G=0.5163 A=0.4837
gnomAD - Genomes Other Sub 2146 G=0.6417 A=0.3583
14KJPN JAPANESE Study-wide 28258 G=0.56080 A=0.43920
8.3KJPN JAPANESE Study-wide 16760 G=0.55967 A=0.44033
1000Genomes_30x Global Study-wide 6404 G=0.6719 A=0.3281
1000Genomes_30x African Sub 1786 G=0.6349 A=0.3651
1000Genomes_30x Europe Sub 1266 G=0.7243 A=0.2757
1000Genomes_30x South Asian Sub 1202 G=0.7687 A=0.2313
1000Genomes_30x East Asian Sub 1170 G=0.5333 A=0.4667
1000Genomes_30x American Sub 980 G=0.718 A=0.282
1000Genomes Global Study-wide 5008 G=0.6711 A=0.3289
1000Genomes African Sub 1322 G=0.6286 A=0.3714
1000Genomes East Asian Sub 1008 G=0.5248 A=0.4752
1000Genomes Europe Sub 1006 G=0.7366 A=0.2634
1000Genomes South Asian Sub 978 G=0.783 A=0.217
1000Genomes American Sub 694 G=0.712 A=0.288
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.6752 A=0.3248
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.7071 A=0.2929
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.6839 A=0.3161
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.5918 A=0.4082
HapMap Global Study-wide 1890 G=0.6450 A=0.3550
HapMap American Sub 770 G=0.662 A=0.338
HapMap African Sub 690 G=0.629 A=0.371
HapMap Asian Sub 254 G=0.555 A=0.445
HapMap Europe Sub 176 G=0.761 A=0.239
Korean Genome Project KOREAN Study-wide 1832 G=0.5895 A=0.4105
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.705 A=0.295
Northern Sweden ACPOP Study-wide 600 G=0.678 A=0.322
SGDP_PRJ Global Study-wide 294 G=0.388 A=0.612
Qatari Global Study-wide 216 G=0.713 A=0.287
A Vietnamese Genetic Variation Database Global Study-wide 214 G=0.486 A=0.514
The Danish reference pan genome Danish Study-wide 40 G=0.72 A=0.28
Siberian Global Study-wide 34 G=0.38 A=0.62
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 10 NC_000010.11:g.119650514G>A
GRCh37.p13 chr 10 NC_000010.10:g.121410026G>A
BAG3 RefSeqGene (LRG_742) NG_016125.1:g.4145G>A
Gene: BAG3, BAG cochaperone 3 (plus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
BAG3 transcript NM_004281.4:c. N/A Upstream Transcript Variant
BAG3 transcript variant X1 XM_005270287.2:c. 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.

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 10 NC_000010.11:g.119650514= NC_000010.11:g.119650514G>A
GRCh37.p13 chr 10 NC_000010.10:g.121410026= NC_000010.10:g.121410026G>A
BAG3 RefSeqGene (LRG_742) NG_016125.1:g.4145= NG_016125.1:g.4145G>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#.

100 SubSNP, 20 Frequency submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss3388862 Sep 28, 2001 (100)
2 TSC-CSHL ss5157004 Oct 08, 2002 (108)
3 SC_JCM ss5688676 Feb 20, 2003 (111)
4 SC_SNP ss15580726 Feb 27, 2004 (120)
5 ABI ss39697836 Mar 14, 2006 (126)
6 ILLUMINA ss75171792 Dec 07, 2007 (129)
7 HUMANGENOME_JCVI ss97689328 Feb 05, 2009 (130)
8 BGI ss106706396 Feb 05, 2009 (130)
9 1000GENOMES ss109799270 Jan 24, 2009 (130)
10 1000GENOMES ss113904331 Jan 25, 2009 (130)
11 KRIBB_YJKIM ss119434572 Dec 01, 2009 (131)
12 ENSEMBL ss143509218 Dec 01, 2009 (131)
13 ILLUMINA ss160546163 Dec 01, 2009 (131)
14 COMPLETE_GENOMICS ss168771994 Jul 04, 2010 (132)
15 COMPLETE_GENOMICS ss171209023 Jul 04, 2010 (132)
16 ILLUMINA ss173337823 Jul 04, 2010 (132)
17 1000GENOMES ss224975321 Jul 14, 2010 (132)
18 1000GENOMES ss235357688 Jul 15, 2010 (132)
19 1000GENOMES ss242028754 Jul 15, 2010 (132)
20 GMI ss280796442 May 04, 2012 (137)
21 PJP ss290944699 May 09, 2011 (134)
22 ILLUMINA ss480564550 May 04, 2012 (137)
23 ILLUMINA ss480578990 May 04, 2012 (137)
24 ILLUMINA ss481398916 Sep 08, 2015 (146)
25 ILLUMINA ss485077877 May 04, 2012 (137)
26 ILLUMINA ss537089218 Sep 08, 2015 (146)
27 TISHKOFF ss562250430 Apr 25, 2013 (138)
28 SSMP ss657463704 Apr 25, 2013 (138)
29 ILLUMINA ss778495699 Sep 08, 2015 (146)
30 ILLUMINA ss782985225 Sep 08, 2015 (146)
31 ILLUMINA ss783946158 Sep 08, 2015 (146)
32 ILLUMINA ss832241884 Sep 08, 2015 (146)
33 ILLUMINA ss833951751 Sep 08, 2015 (146)
34 EVA-GONL ss987988374 Aug 21, 2014 (142)
35 JMKIDD_LAB ss1077346402 Aug 21, 2014 (142)
36 1000GENOMES ss1339321471 Aug 21, 2014 (142)
37 DDI ss1426462293 Apr 01, 2015 (144)
38 EVA_GENOME_DK ss1575392928 Apr 01, 2015 (144)
39 EVA_DECODE ss1597667422 Apr 01, 2015 (144)
40 EVA_UK10K_ALSPAC ss1625574808 Apr 01, 2015 (144)
41 EVA_UK10K_TWINSUK ss1668568841 Apr 01, 2015 (144)
42 EVA_SVP ss1713216347 Apr 01, 2015 (144)
43 ILLUMINA ss1751950536 Sep 08, 2015 (146)
44 HAMMER_LAB ss1806597241 Sep 08, 2015 (146)
45 WEILL_CORNELL_DGM ss1931345817 Feb 12, 2016 (147)
46 GENOMED ss1967238893 Jul 19, 2016 (147)
47 JJLAB ss2026409045 Sep 14, 2016 (149)
48 USC_VALOUEV ss2154685878 Dec 20, 2016 (150)
49 HUMAN_LONGEVITY ss2178612291 Dec 20, 2016 (150)
50 SYSTEMSBIOZJU ss2627671313 Nov 08, 2017 (151)
51 ILLUMINA ss2632770364 Nov 08, 2017 (151)
52 GRF ss2698946320 Nov 08, 2017 (151)
53 GNOMAD ss2894118349 Nov 08, 2017 (151)
54 SWEGEN ss3007251003 Nov 08, 2017 (151)
55 BIOINF_KMB_FNS_UNIBA ss3026993088 Nov 08, 2017 (151)
56 CSHL ss3349339653 Nov 08, 2017 (151)
57 ILLUMINA ss3626548939 Oct 12, 2018 (152)
58 ILLUMINA ss3630792132 Oct 12, 2018 (152)
59 ILLUMINA ss3632967033 Oct 12, 2018 (152)
60 ILLUMINA ss3633664952 Oct 12, 2018 (152)
61 ILLUMINA ss3634427190 Oct 12, 2018 (152)
62 ILLUMINA ss3635357062 Oct 12, 2018 (152)
63 ILLUMINA ss3636111859 Oct 12, 2018 (152)
64 ILLUMINA ss3637107810 Oct 12, 2018 (152)
65 ILLUMINA ss3637877827 Oct 12, 2018 (152)
66 ILLUMINA ss3640134531 Oct 12, 2018 (152)
67 ILLUMINA ss3642878761 Oct 12, 2018 (152)
68 URBANLAB ss3649480194 Oct 12, 2018 (152)
69 EGCUT_WGS ss3674669693 Jul 13, 2019 (153)
70 EVA_DECODE ss3690808212 Jul 13, 2019 (153)
71 ACPOP ss3737733994 Jul 13, 2019 (153)
72 ILLUMINA ss3744728163 Jul 13, 2019 (153)
73 EVA ss3748683469 Jul 13, 2019 (153)
74 ILLUMINA ss3772228398 Jul 13, 2019 (153)
75 PACBIO ss3786804780 Jul 13, 2019 (153)
76 PACBIO ss3791964359 Jul 13, 2019 (153)
77 PACBIO ss3796846495 Jul 13, 2019 (153)
78 KHV_HUMAN_GENOMES ss3814040490 Jul 13, 2019 (153)
79 EVA ss3832364339 Apr 26, 2020 (154)
80 EVA ss3839723258 Apr 26, 2020 (154)
81 EVA ss3845197927 Apr 26, 2020 (154)
82 SGDP_PRJ ss3875189130 Apr 26, 2020 (154)
83 KRGDB ss3923366643 Apr 26, 2020 (154)
84 KOGIC ss3968801343 Apr 26, 2020 (154)
85 EVA ss4017511354 Apr 26, 2021 (155)
86 TOPMED ss4868734187 Apr 26, 2021 (155)
87 TOMMO_GENOMICS ss5199764776 Apr 26, 2021 (155)
88 1000G_HIGH_COVERAGE ss5285692929 Oct 16, 2022 (156)
89 EVA ss5315507353 Oct 16, 2022 (156)
90 EVA ss5396455005 Oct 16, 2022 (156)
91 HUGCELL_USP ss5481093417 Oct 16, 2022 (156)
92 1000G_HIGH_COVERAGE ss5580486022 Oct 16, 2022 (156)
93 SANFORD_IMAGENETICS ss5650224677 Oct 16, 2022 (156)
94 TOMMO_GENOMICS ss5746219889 Oct 16, 2022 (156)
95 EVA ss5799826945 Oct 16, 2022 (156)
96 YY_MCH ss5811938927 Oct 16, 2022 (156)
97 EVA ss5825046099 Oct 16, 2022 (156)
98 EVA ss5849768049 Oct 16, 2022 (156)
99 EVA ss5880790788 Oct 16, 2022 (156)
100 EVA ss5941531199 Oct 16, 2022 (156)
101 1000Genomes NC_000010.10 - 121410026 Oct 12, 2018 (152)
102 1000Genomes_30x NC_000010.11 - 119650514 Oct 16, 2022 (156)
103 The Avon Longitudinal Study of Parents and Children NC_000010.10 - 121410026 Oct 12, 2018 (152)
104 Genetic variation in the Estonian population NC_000010.10 - 121410026 Oct 12, 2018 (152)
105 The Danish reference pan genome NC_000010.10 - 121410026 Apr 26, 2020 (154)
106 gnomAD - Genomes NC_000010.11 - 119650514 Apr 26, 2021 (155)
107 Genome of the Netherlands Release 5 NC_000010.10 - 121410026 Apr 26, 2020 (154)
108 HapMap NC_000010.11 - 119650514 Apr 26, 2020 (154)
109 KOREAN population from KRGDB NC_000010.10 - 121410026 Apr 26, 2020 (154)
110 Korean Genome Project NC_000010.11 - 119650514 Apr 26, 2020 (154)
111 Northern Sweden NC_000010.10 - 121410026 Jul 13, 2019 (153)
112 Qatari NC_000010.10 - 121410026 Apr 26, 2020 (154)
113 SGDP_PRJ NC_000010.10 - 121410026 Apr 26, 2020 (154)
114 Siberian NC_000010.10 - 121410026 Apr 26, 2020 (154)
115 8.3KJPN NC_000010.10 - 121410026 Apr 26, 2021 (155)
116 14KJPN NC_000010.11 - 119650514 Oct 16, 2022 (156)
117 TopMed NC_000010.11 - 119650514 Apr 26, 2021 (155)
118 UK 10K study - Twins NC_000010.10 - 121410026 Oct 12, 2018 (152)
119 A Vietnamese Genetic Variation Database NC_000010.10 - 121410026 Jul 13, 2019 (153)
120 ALFA NC_000010.11 - 119650514 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
ss109799270, ss113904331, ss168771994, ss171209023, ss280796442, ss290944699, ss480564550, ss1597667422, ss1713216347, ss3642878761 NC_000010.9:121400015:G:A NC_000010.11:119650513:G:A (self)
51777760, 28762255, 20407941, 2352482, 12818439, 30544037, 11018859, 13387747, 27206110, 7202232, 57734083, 28762255, 6381351, ss224975321, ss235357688, ss242028754, ss480578990, ss481398916, ss485077877, ss537089218, ss562250430, ss657463704, ss778495699, ss782985225, ss783946158, ss832241884, ss833951751, ss987988374, ss1077346402, ss1339321471, ss1426462293, ss1575392928, ss1625574808, ss1668568841, ss1751950536, ss1806597241, ss1931345817, ss1967238893, ss2026409045, ss2154685878, ss2627671313, ss2632770364, ss2698946320, ss2894118349, ss3007251003, ss3349339653, ss3626548939, ss3630792132, ss3632967033, ss3633664952, ss3634427190, ss3635357062, ss3636111859, ss3637107810, ss3637877827, ss3640134531, ss3674669693, ss3737733994, ss3744728163, ss3748683469, ss3772228398, ss3786804780, ss3791964359, ss3796846495, ss3832364339, ss3839723258, ss3875189130, ss3923366643, ss4017511354, ss5199764776, ss5315507353, ss5396455005, ss5650224677, ss5799826945, ss5825046099, ss5941531199 NC_000010.10:121410025:G:A NC_000010.11:119650513:G:A (self)
68011957, 365838956, 506635, 25179344, 80056993, 84279842, 707003051, ss2178612291, ss3026993088, ss3649480194, ss3690808212, ss3814040490, ss3845197927, ss3968801343, ss4868734187, ss5285692929, ss5481093417, ss5580486022, ss5746219889, ss5811938927, ss5849768049, ss5880790788 NC_000010.11:119650513:G:A NC_000010.11:119650513:G:A (self)
ss15580726 NT_030059.11:40158551:G:A NC_000010.11:119650513:G:A (self)
ss3388862, ss5157004, ss5688676, ss39697836, ss75171792, ss97689328, ss106706396, ss119434572, ss143509218, ss160546163, ss173337823 NT_030059.13:72214489:G:A NC_000010.11:119650513: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 rs2420641

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