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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.

rs12498159

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr4:162492079 (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
C>A / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.252563 (66851/264690, TOPMED)
T=0.251232 (35165/139970, GnomAD)
T=0.39005 (11022/28258, 14KJPN) (+ 17 more)
T=0.39087 (6551/16760, 8.3KJPN)
T=0.13861 (1910/13780, ALFA)
T=0.2829 (1812/6404, 1000G_30x)
T=0.2891 (1448/5008, 1000G)
T=0.2679 (1200/4480, Estonian)
T=0.2893 (1115/3854, ALSPAC)
T=0.2840 (1053/3708, TWINSUK)
T=0.4355 (1276/2930, KOREAN)
T=0.4214 (772/1832, Korea1K)
T=0.285 (284/998, GoNL)
T=0.283 (170/600, NorthernSweden)
C=0.386 (112/290, SGDP_PRJ)
T=0.329 (71/216, Qatari)
C=0.468 (101/216, Vietnamese)
T=0.059 (7/118, HapMap)
T=0.28 (11/40, GENOME_DK)
C=0.46 (12/26, 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 13780 C=0.86139 A=0.00000, T=0.13861
European Sub 10520 C=0.82633 A=0.00000, T=0.17367
African Sub 2450 C=0.9963 A=0.0000, T=0.0037
African Others Sub 102 C=1.000 A=0.000, T=0.000
African American Sub 2348 C=0.9962 A=0.0000, T=0.0038
Asian Sub 30 C=0.97 A=0.00, T=0.03
East Asian Sub 22 C=1.00 A=0.00, T=0.00
Other Asian Sub 8 C=0.9 A=0.0, T=0.1
Latin American 1 Sub 64 C=1.00 A=0.00, T=0.00
Latin American 2 Sub 184 C=1.000 A=0.000, T=0.000
South Asian Sub 58 C=0.95 A=0.00, T=0.05
Other Sub 474 C=0.852 A=0.000, T=0.148


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 C=0.747437 T=0.252563
gnomAD - Genomes Global Study-wide 139970 C=0.748768 T=0.251232
gnomAD - Genomes European Sub 75800 C=0.69719 T=0.30281
gnomAD - Genomes African Sub 41948 C=0.90309 T=0.09691
gnomAD - Genomes American Sub 13626 C=0.62961 T=0.37039
gnomAD - Genomes Ashkenazi Jewish Sub 3322 C=0.6933 T=0.3067
gnomAD - Genomes East Asian Sub 3126 C=0.5186 T=0.4814
gnomAD - Genomes Other Sub 2148 C=0.7318 T=0.2682
14KJPN JAPANESE Study-wide 28258 C=0.60995 T=0.39005
8.3KJPN JAPANESE Study-wide 16760 C=0.60913 T=0.39087
Allele Frequency Aggregator Total Global 13780 C=0.86139 A=0.00000, T=0.13861
Allele Frequency Aggregator European Sub 10520 C=0.82633 A=0.00000, T=0.17367
Allele Frequency Aggregator African Sub 2450 C=0.9963 A=0.0000, T=0.0037
Allele Frequency Aggregator Other Sub 474 C=0.852 A=0.000, T=0.148
Allele Frequency Aggregator Latin American 2 Sub 184 C=1.000 A=0.000, T=0.000
Allele Frequency Aggregator Latin American 1 Sub 64 C=1.00 A=0.00, T=0.00
Allele Frequency Aggregator South Asian Sub 58 C=0.95 A=0.00, T=0.05
Allele Frequency Aggregator Asian Sub 30 C=0.97 A=0.00, T=0.03
1000Genomes_30x Global Study-wide 6404 C=0.7171 T=0.2829
1000Genomes_30x African Sub 1786 C=0.9390 T=0.0610
1000Genomes_30x Europe Sub 1266 C=0.6777 T=0.3223
1000Genomes_30x South Asian Sub 1202 C=0.7055 T=0.2945
1000Genomes_30x East Asian Sub 1170 C=0.5735 T=0.4265
1000Genomes_30x American Sub 980 C=0.549 T=0.451
1000Genomes Global Study-wide 5008 C=0.7109 T=0.2891
1000Genomes African Sub 1322 C=0.9418 T=0.0582
1000Genomes East Asian Sub 1008 C=0.5764 T=0.4236
1000Genomes Europe Sub 1006 C=0.6730 T=0.3270
1000Genomes South Asian Sub 978 C=0.698 T=0.302
1000Genomes American Sub 694 C=0.539 T=0.461
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.7321 T=0.2679
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.7107 T=0.2893
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.7160 T=0.2840
KOREAN population from KRGDB KOREAN Study-wide 2930 C=0.5645 T=0.4355
Korean Genome Project KOREAN Study-wide 1832 C=0.5786 T=0.4214
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.715 T=0.285
Northern Sweden ACPOP Study-wide 600 C=0.717 T=0.283
SGDP_PRJ Global Study-wide 290 C=0.386 T=0.614
Qatari Global Study-wide 216 C=0.671 T=0.329
A Vietnamese Genetic Variation Database Global Study-wide 216 C=0.468 T=0.532
HapMap Global Study-wide 118 C=0.941 T=0.059
HapMap African Sub 118 C=0.941 T=0.059
The Danish reference pan genome Danish Study-wide 40 C=0.72 T=0.28
Siberian Global Study-wide 26 C=0.46 T=0.54
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 4 NC_000004.12:g.162492079C>A
GRCh38.p14 chr 4 NC_000004.12:g.162492079C>T
GRCh37.p13 chr 4 NC_000004.11:g.163413231C>A
GRCh37.p13 chr 4 NC_000004.11:g.163413231C>T
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 C= A T
GRCh38.p14 chr 4 NC_000004.12:g.162492079= NC_000004.12:g.162492079C>A NC_000004.12:g.162492079C>T
GRCh37.p13 chr 4 NC_000004.11:g.163413231= NC_000004.11:g.163413231C>A NC_000004.11:g.163413231C>T
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, 20 Frequency submissions
No Submitter Submission ID Date (Build)
1 CSHL-HAPMAP ss19554377 Feb 28, 2004 (120)
2 SSAHASNP ss22036734 Apr 05, 2004 (121)
3 ABI ss42390135 Mar 15, 2006 (126)
4 HUMANGENOME_JCVI ss99033328 Feb 03, 2009 (130)
5 BGI ss105880820 Feb 03, 2009 (130)
6 1000GENOMES ss108527118 Jan 23, 2009 (130)
7 ENSEMBL ss135064219 Dec 01, 2009 (131)
8 GMI ss154522751 Dec 01, 2009 (131)
9 COMPLETE_GENOMICS ss162734479 Jul 04, 2010 (132)
10 COMPLETE_GENOMICS ss167373989 Jul 04, 2010 (132)
11 BUSHMAN ss199453353 Jul 04, 2010 (132)
12 BCM-HGSC-SUB ss206502911 Jul 04, 2010 (132)
13 1000GENOMES ss221335972 Jul 14, 2010 (132)
14 1000GENOMES ss232690617 Jul 14, 2010 (132)
15 1000GENOMES ss239918187 Jul 15, 2010 (132)
16 GMI ss278023873 May 04, 2012 (137)
17 GMI ss285049418 Apr 25, 2013 (138)
18 PJP ss293241951 May 09, 2011 (134)
19 TISHKOFF ss557998006 Apr 25, 2013 (138)
20 SSMP ss651821625 Apr 25, 2013 (138)
21 EVA-GONL ss980921378 Aug 21, 2014 (142)
22 JMKIDD_LAB ss1072140795 Aug 21, 2014 (142)
23 1000GENOMES ss1312730028 Aug 21, 2014 (142)
24 EVA_GENOME_DK ss1580872747 Apr 01, 2015 (144)
25 EVA_DECODE ss1590437714 Apr 01, 2015 (144)
26 EVA_UK10K_ALSPAC ss1611655799 Apr 01, 2015 (144)
27 EVA_UK10K_TWINSUK ss1654649832 Apr 01, 2015 (144)
28 HAMMER_LAB ss1802511855 Sep 08, 2015 (146)
29 WEILL_CORNELL_DGM ss1924162025 Feb 12, 2016 (147)
30 GENOMED ss1969928406 Jul 19, 2016 (147)
31 JJLAB ss2022669659 Sep 14, 2016 (149)
32 USC_VALOUEV ss2150801613 Dec 20, 2016 (150)
33 HUMAN_LONGEVITY ss2269031174 Dec 20, 2016 (150)
34 SYSTEMSBIOZJU ss2625829383 Nov 08, 2017 (151)
35 GRF ss2706303289 Nov 08, 2017 (151)
36 GNOMAD ss2817879914 Nov 08, 2017 (151)
37 SWEGEN ss2995925091 Nov 08, 2017 (151)
38 BIOINF_KMB_FNS_UNIBA ss3025113464 Nov 08, 2017 (151)
39 CSHL ss3346069807 Nov 08, 2017 (151)
40 URBANLAB ss3647903066 Oct 12, 2018 (152)
41 EGCUT_WGS ss3663839147 Jul 13, 2019 (153)
42 EVA_DECODE ss3713506878 Jul 13, 2019 (153)
43 ACPOP ss3731808027 Jul 13, 2019 (153)
44 EVA ss3762689707 Jul 13, 2019 (153)
45 PACBIO ss3784927193 Jul 13, 2019 (153)
46 PACBIO ss3790354015 Jul 13, 2019 (153)
47 PACBIO ss3795229632 Jul 13, 2019 (153)
48 KHV_HUMAN_GENOMES ss3805849666 Jul 13, 2019 (153)
49 EVA ss3828926303 Apr 26, 2020 (154)
50 EVA ss3837914561 Apr 26, 2020 (154)
51 EVA ss3843355489 Apr 26, 2020 (154)
52 SGDP_PRJ ss3860535840 Apr 26, 2020 (154)
53 KRGDB ss3906897613 Apr 26, 2020 (154)
54 KOGIC ss3955547845 Apr 26, 2020 (154)
55 TOPMED ss4639994668 Apr 26, 2021 (155)
56 TOMMO_GENOMICS ss5169038143 Apr 26, 2021 (155)
57 1000G_HIGH_COVERAGE ss5261822235 Oct 13, 2022 (156)
58 EVA ss5353760857 Oct 13, 2022 (156)
59 HUGCELL_USP ss5460293565 Oct 13, 2022 (156)
60 1000G_HIGH_COVERAGE ss5544351628 Oct 13, 2022 (156)
61 SANFORD_IMAGENETICS ss5636561526 Oct 13, 2022 (156)
62 TOMMO_GENOMICS ss5704315090 Oct 13, 2022 (156)
63 YY_MCH ss5805737125 Oct 13, 2022 (156)
64 EVA ss5845029765 Oct 13, 2022 (156)
65 EVA ss5854541261 Oct 13, 2022 (156)
66 EVA ss5866417968 Oct 13, 2022 (156)
67 EVA ss5964970529 Oct 13, 2022 (156)
68 1000Genomes NC_000004.11 - 163413231 Oct 12, 2018 (152)
69 1000Genomes_30x NC_000004.12 - 162492079 Oct 13, 2022 (156)
70 The Avon Longitudinal Study of Parents and Children NC_000004.11 - 163413231 Oct 12, 2018 (152)
71 Genetic variation in the Estonian population NC_000004.11 - 163413231 Oct 12, 2018 (152)
72 The Danish reference pan genome NC_000004.11 - 163413231 Apr 26, 2020 (154)
73 gnomAD - Genomes NC_000004.12 - 162492079 Apr 26, 2021 (155)
74 Genome of the Netherlands Release 5 NC_000004.11 - 163413231 Apr 26, 2020 (154)
75 HapMap NC_000004.12 - 162492079 Apr 26, 2020 (154)
76 KOREAN population from KRGDB NC_000004.11 - 163413231 Apr 26, 2020 (154)
77 Korean Genome Project NC_000004.12 - 162492079 Apr 26, 2020 (154)
78 Northern Sweden NC_000004.11 - 163413231 Jul 13, 2019 (153)
79 Qatari NC_000004.11 - 163413231 Apr 26, 2020 (154)
80 SGDP_PRJ NC_000004.11 - 163413231 Apr 26, 2020 (154)
81 Siberian NC_000004.11 - 163413231 Apr 26, 2020 (154)
82 8.3KJPN NC_000004.11 - 163413231 Apr 26, 2021 (155)
83 14KJPN NC_000004.12 - 162492079 Oct 13, 2022 (156)
84 TopMed NC_000004.12 - 162492079 Apr 26, 2021 (155)
85 UK 10K study - Twins NC_000004.11 - 163413231 Oct 12, 2018 (152)
86 A Vietnamese Genetic Variation Database NC_000004.11 - 163413231 Jul 13, 2019 (153)
87 ALFA NC_000004.12 - 162492079 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
6663386958 NC_000004.12:162492078:C:A NC_000004.12:162492078:C:A (self)
ss108527118, ss162734479, ss167373989, ss199453353, ss206502911, ss278023873, ss285049418, ss293241951, ss1590437714 NC_000004.10:163632680:C:T NC_000004.12:162492078:C:T (self)
24239978, 13483481, 9577395, 7037686, 5973198, 14075007, 5092892, 6203955, 12552820, 3317967, 27007450, 13483481, 2977155, ss221335972, ss232690617, ss239918187, ss557998006, ss651821625, ss980921378, ss1072140795, ss1312730028, ss1580872747, ss1611655799, ss1654649832, ss1802511855, ss1924162025, ss1969928406, ss2022669659, ss2150801613, ss2625829383, ss2706303289, ss2817879914, ss2995925091, ss3346069807, ss3663839147, ss3731808027, ss3762689707, ss3784927193, ss3790354015, ss3795229632, ss3828926303, ss3837914561, ss3860535840, ss3906897613, ss5169038143, ss5353760857, ss5636561526, ss5845029765, ss5964970529 NC_000004.11:163413230:C:T NC_000004.12:162492078:C:T (self)
31877563, 171673501, 2749714, 11925846, 38152194, 477372224, 6663386958, ss2269031174, ss3025113464, ss3647903066, ss3713506878, ss3805849666, ss3843355489, ss3955547845, ss4639994668, ss5261822235, ss5460293565, ss5544351628, ss5704315090, ss5805737125, ss5854541261, ss5866417968 NC_000004.12:162492078:C:T NC_000004.12:162492078:C:T (self)
ss42390135, ss99033328, ss105880820, ss135064219, ss154522751 NT_016354.19:87960951:C:T NC_000004.12:162492078:C:T (self)
ss19554377, ss22036734 NT_016606.16:24961286:C:T NC_000004.12:162492078:C: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 rs12498159

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