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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.

rs10874498

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:101625394 (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
A>G
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.236677 (62646/264690, TOPMED)
A=0.232300 (32516/139974, GnomAD)
A=0.22033 (4162/18890, ALFA) (+ 15 more)
A=0.33156 (5557/16760, 8.3KJPN)
A=0.2991 (1498/5008, 1000G)
A=0.1913 (857/4480, Estonian)
A=0.2270 (875/3854, ALSPAC)
A=0.2314 (858/3708, TWINSUK)
A=0.3413 (1000/2930, KOREAN)
A=0.3401 (623/1832, Korea1K)
A=0.209 (209/998, GoNL)
A=0.175 (105/600, NorthernSweden)
A=0.215 (106/492, SGDP_PRJ)
A=0.222 (48/216, Qatari)
A=0.360 (77/214, Vietnamese)
A=0.277 (56/202, HapMap)
A=0.22 (12/54, Siberian)
A=0.17 (7/40, GENOME_DK)
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 1 NC_000001.11:g.101625394A>G
GRCh37.p13 chr 1 NC_000001.10:g.102090950A>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

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 18890 A=0.22033 G=0.77967
European Sub 14286 A=0.20867 G=0.79133
African Sub 2946 A=0.2508 G=0.7492
African Others Sub 114 A=0.228 G=0.772
African American Sub 2832 A=0.2518 G=0.7482
Asian Sub 112 A=0.357 G=0.643
East Asian Sub 86 A=0.37 G=0.63
Other Asian Sub 26 A=0.31 G=0.69
Latin American 1 Sub 146 A=0.247 G=0.753
Latin American 2 Sub 610 A=0.257 G=0.743
South Asian Sub 98 A=0.39 G=0.61
Other Sub 692 A=0.247 G=0.753


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=0.236677 G=0.763323
gnomAD - Genomes Global Study-wide 139974 A=0.232300 G=0.767700
gnomAD - Genomes European Sub 75856 A=0.22254 G=0.77746
gnomAD - Genomes African Sub 41908 A=0.24034 G=0.75966
gnomAD - Genomes American Sub 13626 A=0.24739 G=0.75261
gnomAD - Genomes Ashkenazi Jewish Sub 3320 A=0.1669 G=0.8331
gnomAD - Genomes East Asian Sub 3114 A=0.3494 G=0.6506
gnomAD - Genomes Other Sub 2150 A=0.2558 G=0.7442
Allele Frequency Aggregator Total Global 18890 A=0.22033 G=0.77967
Allele Frequency Aggregator European Sub 14286 A=0.20867 G=0.79133
Allele Frequency Aggregator African Sub 2946 A=0.2508 G=0.7492
Allele Frequency Aggregator Other Sub 692 A=0.247 G=0.753
Allele Frequency Aggregator Latin American 2 Sub 610 A=0.257 G=0.743
Allele Frequency Aggregator Latin American 1 Sub 146 A=0.247 G=0.753
Allele Frequency Aggregator Asian Sub 112 A=0.357 G=0.643
Allele Frequency Aggregator South Asian Sub 98 A=0.39 G=0.61
8.3KJPN JAPANESE Study-wide 16760 A=0.33156 G=0.66844
1000Genomes Global Study-wide 5008 A=0.2991 G=0.7009
1000Genomes African Sub 1322 A=0.2511 G=0.7489
1000Genomes East Asian Sub 1008 A=0.3532 G=0.6468
1000Genomes Europe Sub 1006 A=0.2147 G=0.7853
1000Genomes South Asian Sub 978 A=0.392 G=0.608
1000Genomes American Sub 694 A=0.304 G=0.696
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.1913 G=0.8087
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.2270 G=0.7730
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.2314 G=0.7686
KOREAN population from KRGDB KOREAN Study-wide 2930 A=0.3413 G=0.6587
Korean Genome Project KOREAN Study-wide 1832 A=0.3401 G=0.6599
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.209 G=0.791
Northern Sweden ACPOP Study-wide 600 A=0.175 G=0.825
SGDP_PRJ Global Study-wide 492 A=0.215 G=0.785
Qatari Global Study-wide 216 A=0.222 G=0.778
A Vietnamese Genetic Variation Database Global Study-wide 214 A=0.360 G=0.640
HapMap Global Study-wide 202 A=0.277 G=0.723
HapMap African Sub 118 A=0.212 G=0.788
HapMap Asian Sub 84 A=0.37 G=0.63
Siberian Global Study-wide 54 A=0.22 G=0.78
The Danish reference pan genome Danish Study-wide 40 A=0.17 G=0.82
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.p13 chr 1 NC_000001.11:g.101625394= NC_000001.11:g.101625394A>G
GRCh37.p13 chr 1 NC_000001.10:g.102090950= NC_000001.10:g.102090950A>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#.

70 SubSNP, 18 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss15425280 Feb 27, 2004 (120)
2 SC_SNP ss18069721 Feb 27, 2004 (120)
3 SC_SNP ss18135803 Feb 27, 2004 (120)
4 SSAHASNP ss20429444 Apr 05, 2004 (121)
5 ABI ss41113016 Mar 13, 2006 (126)
6 HGSV ss78345191 Dec 06, 2007 (129)
7 HGSV ss79867842 Dec 15, 2007 (130)
8 HGSV ss85498897 Dec 15, 2007 (130)
9 BCMHGSC_JDW ss87665697 Mar 23, 2008 (129)
10 HUMANGENOME_JCVI ss97962471 Feb 05, 2009 (130)
11 BGI ss102769346 Feb 20, 2009 (131)
12 1000GENOMES ss108465678 Jan 23, 2009 (130)
13 1000GENOMES ss110912881 Jan 25, 2009 (130)
14 ILLUMINA-UK ss118928347 Dec 01, 2009 (131)
15 ENSEMBL ss131631007 Dec 01, 2009 (131)
16 ENSEMBL ss138047516 Dec 01, 2009 (131)
17 GMI ss155433708 Dec 01, 2009 (131)
18 COMPLETE_GENOMICS ss163768062 Jul 04, 2010 (132)
19 COMPLETE_GENOMICS ss164893846 Jul 04, 2010 (132)
20 COMPLETE_GENOMICS ss166918924 Jul 04, 2010 (132)
21 BUSHMAN ss198849841 Jul 04, 2010 (132)
22 BCM-HGSC-SUB ss205300990 Jul 04, 2010 (132)
23 1000GENOMES ss218557032 Jul 14, 2010 (132)
24 1000GENOMES ss230662750 Jul 14, 2010 (132)
25 1000GENOMES ss238328192 Jul 15, 2010 (132)
26 BL ss253325399 May 09, 2011 (134)
27 GMI ss275950708 May 04, 2012 (137)
28 GMI ss284108332 Apr 25, 2013 (138)
29 PJP ss290583371 May 09, 2011 (134)
30 TISHKOFF ss554495802 Apr 25, 2013 (138)
31 SSMP ss648264131 Apr 25, 2013 (138)
32 EVA-GONL ss975498412 Aug 21, 2014 (142)
33 JMKIDD_LAB ss1068138934 Aug 21, 2014 (142)
34 1000GENOMES ss1292163111 Aug 21, 2014 (142)
35 DDI ss1425915633 Apr 01, 2015 (144)
36 EVA_GENOME_DK ss1574280758 Apr 01, 2015 (144)
37 EVA_DECODE ss1584876700 Apr 01, 2015 (144)
38 EVA_UK10K_ALSPAC ss1600848268 Apr 01, 2015 (144)
39 EVA_UK10K_TWINSUK ss1643842301 Apr 01, 2015 (144)
40 HAMMER_LAB ss1794831395 Sep 08, 2015 (146)
41 WEILL_CORNELL_DGM ss1918697775 Feb 12, 2016 (147)
42 GENOMED ss1966823731 Jul 19, 2016 (147)
43 JJLAB ss2019871068 Sep 14, 2016 (149)
44 USC_VALOUEV ss2147889433 Dec 20, 2016 (150)
45 HUMAN_LONGEVITY ss2165149424 Dec 20, 2016 (150)
46 TOPMED ss2327501614 Dec 20, 2016 (150)
47 SYSTEMSBIOZJU ss2624445968 Nov 08, 2017 (151)
48 GRF ss2697817166 Nov 08, 2017 (151)
49 GNOMAD ss2758796533 Nov 08, 2017 (151)
50 SWEGEN ss2987328068 Nov 08, 2017 (151)
51 BIOINF_KMB_FNS_UNIBA ss3023698828 Nov 08, 2017 (151)
52 TOPMED ss3085016366 Nov 08, 2017 (151)
53 CSHL ss3343602472 Nov 08, 2017 (151)
54 URBANLAB ss3646734789 Oct 11, 2018 (152)
55 EGCUT_WGS ss3655414921 Jul 12, 2019 (153)
56 EVA_DECODE ss3687395331 Jul 12, 2019 (153)
57 ACPOP ss3727326914 Jul 12, 2019 (153)
58 EVA ss3746591035 Jul 12, 2019 (153)
59 PACBIO ss3783500420 Jul 12, 2019 (153)
60 PACBIO ss3789144700 Jul 12, 2019 (153)
61 PACBIO ss3794017570 Jul 12, 2019 (153)
62 KHV_HUMAN_GENOMES ss3799591301 Jul 12, 2019 (153)
63 EVA ss3826334060 Apr 25, 2020 (154)
64 EVA ss3836557181 Apr 25, 2020 (154)
65 EVA ss3841965262 Apr 25, 2020 (154)
66 SGDP_PRJ ss3849506712 Apr 25, 2020 (154)
67 KRGDB ss3894587481 Apr 25, 2020 (154)
68 KOGIC ss3945117504 Apr 25, 2020 (154)
69 TOPMED ss4461197282 Apr 25, 2021 (155)
70 TOMMO_GENOMICS ss5145376006 Apr 25, 2021 (155)
71 1000Genomes NC_000001.10 - 102090950 Oct 11, 2018 (152)
72 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 102090950 Oct 11, 2018 (152)
73 Genetic variation in the Estonian population NC_000001.10 - 102090950 Oct 11, 2018 (152)
74 The Danish reference pan genome NC_000001.10 - 102090950 Apr 25, 2020 (154)
75 gnomAD - Genomes NC_000001.11 - 101625394 Apr 25, 2021 (155)
76 Genome of the Netherlands Release 5 NC_000001.10 - 102090950 Apr 25, 2020 (154)
77 HapMap NC_000001.11 - 101625394 Apr 25, 2020 (154)
78 KOREAN population from KRGDB NC_000001.10 - 102090950 Apr 25, 2020 (154)
79 Korean Genome Project NC_000001.11 - 101625394 Apr 25, 2020 (154)
80 Northern Sweden NC_000001.10 - 102090950 Jul 12, 2019 (153)
81 Qatari NC_000001.10 - 102090950 Apr 25, 2020 (154)
82 SGDP_PRJ NC_000001.10 - 102090950 Apr 25, 2020 (154)
83 Siberian NC_000001.10 - 102090950 Apr 25, 2020 (154)
84 8.3KJPN NC_000001.10 - 102090950 Apr 25, 2021 (155)
85 TopMed NC_000001.11 - 101625394 Apr 25, 2021 (155)
86 UK 10K study - Twins NC_000001.10 - 102090950 Oct 11, 2018 (152)
87 A Vietnamese Genetic Variation Database NC_000001.10 - 102090950 Jul 12, 2019 (153)
88 ALFA NC_000001.11 - 101625394 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)
rs59619442 May 25, 2008 (130)
rs74202924 Dec 02, 2009 (131)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss78345191, ss79867842, ss85498897 NC_000001.8:101802970:A:G NC_000001.11:101625393:A:G (self)
ss87665697, ss108465678, ss110912881, ss118928347, ss163768062, ss164893846, ss166918924, ss198849841, ss205300990, ss253325399, ss275950708, ss284108332, ss290583371, ss1584876700 NC_000001.9:101863537:A:G NC_000001.11:101625393:A:G (self)
2928810, 1618282, 1153169, 1634783, 702143, 1764875, 611779, 739705, 1523692, 405787, 3345313, 1618282, 348847, ss218557032, ss230662750, ss238328192, ss554495802, ss648264131, ss975498412, ss1068138934, ss1292163111, ss1425915633, ss1574280758, ss1600848268, ss1643842301, ss1794831395, ss1918697775, ss1966823731, ss2019871068, ss2147889433, ss2327501614, ss2624445968, ss2697817166, ss2758796533, ss2987328068, ss3343602472, ss3655414921, ss3727326914, ss3746591035, ss3783500420, ss3789144700, ss3794017570, ss3826334060, ss3836557181, ss3849506712, ss3894587481, ss5145376006 NC_000001.10:102090949:A:G NC_000001.11:101625393:A:G (self)
20706467, 139998, 1495505, 15622775, 24803617, 719583571, ss2165149424, ss3023698828, ss3085016366, ss3646734789, ss3687395331, ss3799591301, ss3841965262, ss3945117504, ss4461197282 NC_000001.11:101625393:A:G NC_000001.11:101625393:A:G (self)
ss15425280, ss18069721, ss18135803, ss20429444 NT_028050.13:10279893:A:G NC_000001.11:101625393:A:G (self)
ss41113016, ss97962471, ss102769346, ss131631007, ss138047516, ss155433708 NT_032977.9:72062867:A:G NC_000001.11:101625393: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 rs10874498

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