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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.

rs10799890

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:162956293 (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
A>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.253323 (67052/264690, TOPMED)
G=0.241453 (33817/140056, GnomAD)
G=0.47958 (13551/28256, 14KJPN) (+ 19 more)
G=0.20932 (5012/23944, ALFA)
G=0.47375 (7940/16760, 8.3KJPN)
G=0.2931 (1877/6404, 1000G_30x)
G=0.3005 (1505/5008, 1000G)
G=0.1373 (615/4480, Estonian)
G=0.1814 (699/3854, ALSPAC)
G=0.1826 (677/3708, TWINSUK)
G=0.4645 (1361/2930, KOREAN)
G=0.3399 (643/1892, HapMap)
G=0.4465 (818/1832, Korea1K)
G=0.192 (192/998, GoNL)
G=0.171 (107/626, Chileans)
G=0.145 (87/600, NorthernSweden)
A=0.345 (98/284, SGDP_PRJ)
G=0.333 (72/216, Qatari)
G=0.410 (87/212, Vietnamese)
G=0.17 (7/40, GENOME_DK)
G=0.20 (8/40, Ancient Sardinia)
A=0.44 (16/36, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
None
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 23944 A=0.79068 G=0.20932
European Sub 15654 A=0.83206 G=0.16794
African Sub 3622 A=0.6358 G=0.3642
African Others Sub 126 A=0.627 G=0.373
African American Sub 3496 A=0.6362 G=0.3638
Asian Sub 160 A=0.694 G=0.306
East Asian Sub 102 A=0.676 G=0.324
Other Asian Sub 58 A=0.72 G=0.28
Latin American 1 Sub 292 A=0.784 G=0.216
Latin American 2 Sub 2768 A=0.7760 G=0.2240
South Asian Sub 110 A=0.718 G=0.282
Other Sub 1338 A=0.7750 G=0.2250


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 A=0.746677 G=0.253323
gnomAD - Genomes Global Study-wide 140056 A=0.758547 G=0.241453
gnomAD - Genomes European Sub 75892 A=0.82496 G=0.17504
gnomAD - Genomes African Sub 41938 A=0.63777 G=0.36223
gnomAD - Genomes American Sub 13634 A=0.78070 G=0.21930
gnomAD - Genomes Ashkenazi Jewish Sub 3324 A=0.8195 G=0.1805
gnomAD - Genomes East Asian Sub 3120 A=0.5968 G=0.4032
gnomAD - Genomes Other Sub 2148 A=0.7700 G=0.2300
14KJPN JAPANESE Study-wide 28256 A=0.52042 G=0.47958
Allele Frequency Aggregator Total Global 23944 A=0.79068 G=0.20932
Allele Frequency Aggregator European Sub 15654 A=0.83206 G=0.16794
Allele Frequency Aggregator African Sub 3622 A=0.6358 G=0.3642
Allele Frequency Aggregator Latin American 2 Sub 2768 A=0.7760 G=0.2240
Allele Frequency Aggregator Other Sub 1338 A=0.7750 G=0.2250
Allele Frequency Aggregator Latin American 1 Sub 292 A=0.784 G=0.216
Allele Frequency Aggregator Asian Sub 160 A=0.694 G=0.306
Allele Frequency Aggregator South Asian Sub 110 A=0.718 G=0.282
8.3KJPN JAPANESE Study-wide 16760 A=0.52625 G=0.47375
1000Genomes_30x Global Study-wide 6404 A=0.7069 G=0.2931
1000Genomes_30x African Sub 1786 A=0.6159 G=0.3841
1000Genomes_30x Europe Sub 1266 A=0.8515 G=0.1485
1000Genomes_30x South Asian Sub 1202 A=0.7496 G=0.2504
1000Genomes_30x East Asian Sub 1170 A=0.5769 G=0.4231
1000Genomes_30x American Sub 980 A=0.789 G=0.211
1000Genomes Global Study-wide 5008 A=0.6995 G=0.3005
1000Genomes African Sub 1322 A=0.6067 G=0.3933
1000Genomes East Asian Sub 1008 A=0.5675 G=0.4325
1000Genomes Europe Sub 1006 A=0.8479 G=0.1521
1000Genomes South Asian Sub 978 A=0.740 G=0.260
1000Genomes American Sub 694 A=0.795 G=0.205
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.8627 G=0.1373
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.8186 G=0.1814
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.8174 G=0.1826
KOREAN population from KRGDB KOREAN Study-wide 2930 A=0.5355 G=0.4645
HapMap Global Study-wide 1892 A=0.6601 G=0.3399
HapMap American Sub 770 A=0.748 G=0.252
HapMap African Sub 692 A=0.577 G=0.423
HapMap Asian Sub 254 A=0.508 G=0.492
HapMap Europe Sub 176 A=0.824 G=0.176
Korean Genome Project KOREAN Study-wide 1832 A=0.5535 G=0.4465
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.808 G=0.192
Chileans Chilean Study-wide 626 A=0.829 G=0.171
Northern Sweden ACPOP Study-wide 600 A=0.855 G=0.145
SGDP_PRJ Global Study-wide 284 A=0.345 G=0.655
Qatari Global Study-wide 216 A=0.667 G=0.333
A Vietnamese Genetic Variation Database Global Study-wide 212 A=0.590 G=0.410
The Danish reference pan genome Danish Study-wide 40 A=0.82 G=0.17
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 40 A=0.80 G=0.20
Siberian Global Study-wide 36 A=0.44 G=0.56
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.162956293A>G
GRCh37.p13 chr 1 NC_000001.10:g.162926083A>G
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 A= G
GRCh38.p14 chr 1 NC_000001.11:g.162956293= NC_000001.11:g.162956293A>G
GRCh37.p13 chr 1 NC_000001.10:g.162926083= NC_000001.10:g.162926083A>G
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#.

67 SubSNP, 22 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss16041331 Feb 27, 2004 (120)
2 SC_SNP ss18136379 Feb 27, 2004 (120)
3 SC_SNP ss18404538 Feb 27, 2004 (120)
4 AFFY ss76678471 Dec 07, 2007 (129)
5 HGSV ss82732142 Dec 15, 2007 (130)
6 KRIBB_YJKIM ss105013774 Feb 06, 2009 (130)
7 1000GENOMES ss108644566 Jan 23, 2009 (130)
8 ILLUMINA-UK ss119059430 Feb 15, 2009 (130)
9 GMI ss155836033 Dec 01, 2009 (131)
10 BUSHMAN ss199160231 Jul 04, 2010 (132)
11 1000GENOMES ss218681010 Jul 14, 2010 (132)
12 1000GENOMES ss230753835 Jul 14, 2010 (132)
13 1000GENOMES ss238397448 Jul 15, 2010 (132)
14 BL ss253555442 May 09, 2011 (134)
15 GMI ss276074726 May 04, 2012 (137)
16 PJP ss290649248 May 09, 2011 (134)
17 TISHKOFF ss554770846 Apr 25, 2013 (138)
18 SSMP ss648453655 Apr 25, 2013 (138)
19 EVA-GONL ss975743808 Aug 21, 2014 (142)
20 JMKIDD_LAB ss1068312836 Aug 21, 2014 (142)
21 1000GENOMES ss1293158789 Aug 21, 2014 (142)
22 DDI ss1425996857 Apr 01, 2015 (144)
23 EVA_GENOME_DK ss1574432481 Apr 01, 2015 (144)
24 EVA_DECODE ss1585127079 Apr 01, 2015 (144)
25 EVA_UK10K_ALSPAC ss1601336851 Apr 01, 2015 (144)
26 EVA_UK10K_TWINSUK ss1644330884 Apr 01, 2015 (144)
27 EVA_SVP ss1712375751 Apr 01, 2015 (144)
28 HAMMER_LAB ss1795171970 Sep 08, 2015 (146)
29 WEILL_CORNELL_DGM ss1918980329 Feb 12, 2016 (147)
30 GENOMED ss1966880829 Jul 19, 2016 (147)
31 JJLAB ss2020004198 Sep 14, 2016 (149)
32 ILLUMINA ss2094981168 Dec 20, 2016 (150)
33 USC_VALOUEV ss2148031060 Dec 20, 2016 (150)
34 HUMAN_LONGEVITY ss2167003021 Dec 20, 2016 (150)
35 SYSTEMSBIOZJU ss2624511169 Nov 08, 2017 (151)
36 GRF ss2698007345 Nov 08, 2017 (151)
37 GNOMAD ss2761984033 Nov 08, 2017 (151)
38 SWEGEN ss2987848863 Nov 08, 2017 (151)
39 BIOINF_KMB_FNS_UNIBA ss3023759386 Nov 08, 2017 (151)
40 CSHL ss3343737663 Nov 08, 2017 (151)
41 ILLUMINA ss3651481657 Oct 11, 2018 (152)
42 EGCUT_WGS ss3655787977 Jul 12, 2019 (153)
43 EVA_DECODE ss3687897777 Jul 12, 2019 (153)
44 ACPOP ss3727536167 Jul 12, 2019 (153)
45 EVA ss3746879004 Jul 12, 2019 (153)
46 KHV_HUMAN_GENOMES ss3799879281 Jul 12, 2019 (153)
47 EVA ss3826454789 Apr 25, 2020 (154)
48 EVA ss3836622452 Apr 25, 2020 (154)
49 EVA ss3842032081 Apr 25, 2020 (154)
50 SGDP_PRJ ss3850126753 Apr 25, 2020 (154)
51 KRGDB ss3895354200 Apr 25, 2020 (154)
52 KOGIC ss3945773719 Apr 25, 2020 (154)
53 EVA ss3984829344 Apr 25, 2021 (155)
54 TOPMED ss4470351165 Apr 25, 2021 (155)
55 TOMMO_GENOMICS ss5146754432 Apr 25, 2021 (155)
56 1000G_HIGH_COVERAGE ss5244495516 Oct 12, 2022 (156)
57 EVA ss5322417857 Oct 12, 2022 (156)
58 HUGCELL_USP ss5445060816 Oct 12, 2022 (156)
59 EVA ss5506048413 Oct 12, 2022 (156)
60 1000G_HIGH_COVERAGE ss5517924221 Oct 12, 2022 (156)
61 SANFORD_IMAGENETICS ss5626706183 Oct 12, 2022 (156)
62 TOMMO_GENOMICS ss5674032536 Oct 12, 2022 (156)
63 YY_MCH ss5801311330 Oct 12, 2022 (156)
64 EVA ss5832745886 Oct 12, 2022 (156)
65 EVA ss5849131960 Oct 12, 2022 (156)
66 EVA ss5910474417 Oct 12, 2022 (156)
67 EVA ss5938503567 Oct 12, 2022 (156)
68 1000Genomes NC_000001.10 - 162926083 Oct 11, 2018 (152)
69 1000Genomes_30x NC_000001.11 - 162956293 Oct 12, 2022 (156)
70 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 162926083 Oct 11, 2018 (152)
71 Chileans NC_000001.10 - 162926083 Apr 25, 2020 (154)
72 Genetic variation in the Estonian population NC_000001.10 - 162926083 Oct 11, 2018 (152)
73 The Danish reference pan genome NC_000001.10 - 162926083 Apr 25, 2020 (154)
74 gnomAD - Genomes NC_000001.11 - 162956293 Apr 25, 2021 (155)
75 Genome of the Netherlands Release 5 NC_000001.10 - 162926083 Apr 25, 2020 (154)
76 HapMap NC_000001.11 - 162956293 Apr 25, 2020 (154)
77 KOREAN population from KRGDB NC_000001.10 - 162926083 Apr 25, 2020 (154)
78 Korean Genome Project NC_000001.11 - 162956293 Apr 25, 2020 (154)
79 Northern Sweden NC_000001.10 - 162926083 Jul 12, 2019 (153)
80 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000001.10 - 162926083 Apr 25, 2021 (155)
81 Qatari NC_000001.10 - 162926083 Apr 25, 2020 (154)
82 SGDP_PRJ NC_000001.10 - 162926083 Apr 25, 2020 (154)
83 Siberian NC_000001.10 - 162926083 Apr 25, 2020 (154)
84 8.3KJPN NC_000001.10 - 162926083 Apr 25, 2021 (155)
85 14KJPN NC_000001.11 - 162956293 Oct 12, 2022 (156)
86 TopMed NC_000001.11 - 162956293 Apr 25, 2021 (155)
87 UK 10K study - Twins NC_000001.10 - 162926083 Oct 11, 2018 (152)
88 A Vietnamese Genetic Variation Database NC_000001.10 - 162926083 Jul 12, 2019 (153)
89 ALFA NC_000001.11 - 162956293 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)
rs60988654 May 26, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss82732142 NC_000001.8:159657740:A:G NC_000001.11:162956292:A:G (self)
ss108644566, ss119059430, ss199160231, ss253555442, ss276074726, ss290649248, ss1585127079, ss1712375751 NC_000001.9:161192706:A:G NC_000001.11:162956292:A:G (self)
3958455, 2155905, 22517, 1526225, 1731899, 937133, 2531594, 821032, 55271, 1022259, 2143733, 547414, 4723739, 2155905, 462097, ss218681010, ss230753835, ss238397448, ss554770846, ss648453655, ss975743808, ss1068312836, ss1293158789, ss1425996857, ss1574432481, ss1601336851, ss1644330884, ss1795171970, ss1918980329, ss1966880829, ss2020004198, ss2094981168, ss2148031060, ss2624511169, ss2698007345, ss2761984033, ss2987848863, ss3343737663, ss3651481657, ss3655787977, ss3727536167, ss3746879004, ss3826454789, ss3836622452, ss3850126753, ss3895354200, ss3984829344, ss5146754432, ss5322417857, ss5506048413, ss5626706183, ss5832745886, ss5938503567 NC_000001.10:162926082:A:G NC_000001.11:162956292:A:G (self)
5450156, 28745637, 188740, 2151720, 7869640, 33957500, 11800726919, ss2167003021, ss3023759386, ss3687897777, ss3799879281, ss3842032081, ss3945773719, ss4470351165, ss5244495516, ss5445060816, ss5517924221, ss5674032536, ss5801311330, ss5849131960, ss5910474417 NC_000001.11:162956292:A:G NC_000001.11:162956292:A:G (self)
ss76678471, ss105013774, ss155836033 NT_004487.19:14414724:A:G NC_000001.11:162956292:A:G (self)
ss16041331, ss18136379, ss18404538 NT_004668.16:1431554:A:G NC_000001.11:162956292:A: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 rs10799890

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