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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.

rs10908421

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:154663409 (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 / G>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.209407 (55428/264690, TOPMED)
T=0.202801 (28408/140078, GnomAD)
T=0.40310 (11390/28256, 14KJPN) (+ 14 more)
T=0.23018 (5785/25132, ALFA)
T=0.40346 (6762/16760, 8.3KJPN)
T=0.1938 (1241/6404, 1000G_30x)
T=0.1969 (986/5008, 1000G)
T=0.2600 (1165/4480, Estonian)
T=0.3454 (1012/2930, KOREAN)
T=0.3668 (672/1832, Korea1K)
T=0.275 (274/998, GoNL)
T=0.253 (152/600, NorthernSweden)
T=0.203 (67/330, HapMap)
T=0.153 (33/216, Qatari)
T=0.313 (67/214, Vietnamese)
G=0.399 (79/198, SGDP_PRJ)
G=0.30 (9/30, 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: 20231103111315
Population Group Sample Size Ref Allele Alt Allele Ref HMOZ Alt HMOZ HTRZ HWEP
Total Global 25132 G=0.76982 T=0.23018 0.597087 0.057457 0.345456 5
European Sub 20288 G=0.74675 T=0.25325 0.556979 0.063486 0.379535 0
African Sub 2946 G=0.9447 T=0.0553 0.893415 0.004073 0.102512 0
African Others Sub 114 G=0.991 T=0.009 0.982456 0.0 0.017544 0
African American Sub 2832 G=0.9428 T=0.0572 0.889831 0.004237 0.105932 0
Asian Sub 112 G=0.679 T=0.321 0.428571 0.071429 0.5 1
East Asian Sub 86 G=0.71 T=0.29 0.465116 0.046512 0.488372 1
Other Asian Sub 26 G=0.58 T=0.42 0.307692 0.153846 0.538462 0
Latin American 1 Sub 146 G=0.767 T=0.233 0.60274 0.068493 0.328767 0
Latin American 2 Sub 610 G=0.643 T=0.357 0.422951 0.137705 0.439344 0
South Asian Sub 98 G=0.84 T=0.16 0.714286 0.040816 0.244898 0
Other Sub 932 G=0.807 T=0.193 0.654506 0.040773 0.304721 0


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=0.790593 T=0.209407
gnomAD - Genomes Global Study-wide 140078 G=0.797199 T=0.202801
gnomAD - Genomes European Sub 75832 G=0.74317 T=0.25683
gnomAD - Genomes African Sub 42010 G=0.94613 T=0.05387
gnomAD - Genomes American Sub 13644 G=0.68484 T=0.31516
gnomAD - Genomes Ashkenazi Jewish Sub 3322 G=0.7736 T=0.2264
gnomAD - Genomes East Asian Sub 3120 G=0.6308 T=0.3692
gnomAD - Genomes Other Sub 2150 G=0.7837 T=0.2163
14KJPN JAPANESE Study-wide 28256 G=0.59690 T=0.40310
Allele Frequency Aggregator Total Global 25132 G=0.76982 T=0.23018
Allele Frequency Aggregator European Sub 20288 G=0.74675 T=0.25325
Allele Frequency Aggregator African Sub 2946 G=0.9447 T=0.0553
Allele Frequency Aggregator Other Sub 932 G=0.807 T=0.193
Allele Frequency Aggregator Latin American 2 Sub 610 G=0.643 T=0.357
Allele Frequency Aggregator Latin American 1 Sub 146 G=0.767 T=0.233
Allele Frequency Aggregator Asian Sub 112 G=0.679 T=0.321
Allele Frequency Aggregator South Asian Sub 98 G=0.84 T=0.16
8.3KJPN JAPANESE Study-wide 16760 G=0.59654 T=0.40346
1000Genomes_30x Global Study-wide 6404 G=0.8062 T=0.1938
1000Genomes_30x African Sub 1786 G=0.9927 T=0.0073
1000Genomes_30x Europe Sub 1266 G=0.7457 T=0.2543
1000Genomes_30x South Asian Sub 1202 G=0.8519 T=0.1481
1000Genomes_30x East Asian Sub 1170 G=0.6701 T=0.3299
1000Genomes_30x American Sub 980 G=0.651 T=0.349
1000Genomes Global Study-wide 5008 G=0.8031 T=0.1969
1000Genomes African Sub 1322 G=0.9917 T=0.0083
1000Genomes East Asian Sub 1008 G=0.6716 T=0.3284
1000Genomes Europe Sub 1006 G=0.7455 T=0.2545
1000Genomes South Asian Sub 978 G=0.856 T=0.144
1000Genomes American Sub 694 G=0.644 T=0.356
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.7400 T=0.2600
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.6546 A=0.0000, T=0.3454
Korean Genome Project KOREAN Study-wide 1832 G=0.6332 T=0.3668
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.725 T=0.275
Northern Sweden ACPOP Study-wide 600 G=0.747 T=0.253
HapMap Global Study-wide 330 G=0.797 T=0.203
HapMap African Sub 120 G=1.000 T=0.000
HapMap American Sub 120 G=0.733 T=0.267
HapMap Asian Sub 90 G=0.61 T=0.39
Qatari Global Study-wide 216 G=0.847 T=0.153
A Vietnamese Genetic Variation Database Global Study-wide 214 G=0.687 T=0.313
SGDP_PRJ Global Study-wide 198 G=0.399 T=0.601
Siberian Global Study-wide 30 G=0.30 T=0.70
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.154663409G>A
GRCh38.p14 chr 1 NC_000001.11:g.154663409G>T
GRCh37.p13 chr 1 NC_000001.10:g.154635885G>A
GRCh37.p13 chr 1 NC_000001.10:g.154635885G>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 G= A T
GRCh38.p14 chr 1 NC_000001.11:g.154663409= NC_000001.11:g.154663409G>A NC_000001.11:g.154663409G>T
GRCh37.p13 chr 1 NC_000001.10:g.154635885= NC_000001.10:g.154635885G>A NC_000001.10:g.154635885G>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#.

62 SubSNP, 17 Frequency submissions
No Submitter Submission ID Date (Build)
1 CSHL-HAPMAP ss16384621 Feb 27, 2004 (120)
2 SC_SNP ss18070064 Feb 27, 2004 (120)
3 SC_SNP ss18243381 Feb 27, 2004 (120)
4 SSAHASNP ss20433955 Apr 05, 2004 (121)
5 ABI ss41239218 Mar 13, 2006 (126)
6 PERLEGEN ss68780540 May 16, 2007 (127)
7 BCMHGSC_JDW ss87824911 Mar 23, 2008 (129)
8 HUMANGENOME_JCVI ss99251191 Feb 06, 2009 (130)
9 BGI ss102785653 Dec 01, 2009 (131)
10 1000GENOMES ss108599863 Jan 23, 2009 (130)
11 ENSEMBL ss131695640 Dec 01, 2009 (131)
12 COMPLETE_GENOMICS ss167134428 Jul 04, 2010 (132)
13 BCM-HGSC-SUB ss205292984 Jul 04, 2010 (132)
14 1000GENOMES ss230732133 Jul 14, 2010 (132)
15 1000GENOMES ss238380007 Jul 15, 2010 (132)
16 GMI ss276051451 May 04, 2012 (137)
17 GMI ss284152766 Apr 25, 2013 (138)
18 PJP ss290637201 May 09, 2011 (134)
19 SSMP ss648414319 Apr 25, 2013 (138)
20 EVA-GONL ss975683065 Aug 21, 2014 (142)
21 JMKIDD_LAB ss1068270004 Aug 21, 2014 (142)
22 1000GENOMES ss1292927740 Aug 21, 2014 (142)
23 DDI ss1425979131 Apr 01, 2015 (144)
24 EVA_DECODE ss1585064533 Apr 01, 2015 (144)
25 WEILL_CORNELL_DGM ss1918916991 Feb 12, 2016 (147)
26 GENOMED ss1966867682 Jul 19, 2016 (147)
27 JJLAB ss2019974030 Sep 14, 2016 (149)
28 USC_VALOUEV ss2147998570 Dec 20, 2016 (150)
29 HUMAN_LONGEVITY ss2166545668 Dec 20, 2016 (150)
30 SYSTEMSBIOZJU ss2624495062 Nov 08, 2017 (151)
31 GRF ss2697971485 Nov 08, 2017 (151)
32 GNOMAD ss2761322205 Nov 08, 2017 (151)
33 AFFY ss2984879337 Nov 08, 2017 (151)
34 AFFY ss2985525113 Nov 08, 2017 (151)
35 SWEGEN ss2987752962 Nov 08, 2017 (151)
36 BIOINF_KMB_FNS_UNIBA ss3023744214 Nov 08, 2017 (151)
37 CSHL ss3343710770 Nov 08, 2017 (151)
38 URBANLAB ss3646791507 Oct 11, 2018 (152)
39 ILLUMINA ss3653648532 Oct 11, 2018 (152)
40 EGCUT_WGS ss3655693208 Jul 12, 2019 (153)
41 EVA_DECODE ss3687783538 Jul 12, 2019 (153)
42 ACPOP ss3727486191 Jul 12, 2019 (153)
43 EVA ss3746808747 Jul 12, 2019 (153)
44 KHV_HUMAN_GENOMES ss3799810413 Jul 12, 2019 (153)
45 EVA ss3826424436 Apr 25, 2020 (154)
46 EVA ss3836606835 Apr 25, 2020 (154)
47 EVA ss3842016060 Apr 25, 2020 (154)
48 SGDP_PRJ ss3850007592 Apr 25, 2020 (154)
49 KRGDB ss3895214296 Apr 25, 2020 (154)
50 KOGIC ss3945652446 Apr 25, 2020 (154)
51 TOPMED ss4468322111 Apr 25, 2021 (155)
52 TOMMO_GENOMICS ss5146485801 Apr 25, 2021 (155)
53 1000G_HIGH_COVERAGE ss5244294929 Oct 12, 2022 (156)
54 HUGCELL_USP ss5444888191 Oct 12, 2022 (156)
55 1000G_HIGH_COVERAGE ss5517624010 Oct 12, 2022 (156)
56 SANFORD_IMAGENETICS ss5626592461 Oct 12, 2022 (156)
57 TOMMO_GENOMICS ss5673682298 Oct 12, 2022 (156)
58 YY_MCH ss5801260574 Oct 12, 2022 (156)
59 EVA ss5832666239 Oct 12, 2022 (156)
60 EVA ss5849109150 Oct 12, 2022 (156)
61 EVA ss5910247941 Oct 12, 2022 (156)
62 EVA ss5938386354 Oct 12, 2022 (156)
63 1000Genomes NC_000001.10 - 154635885 Oct 11, 2018 (152)
64 1000Genomes_30x NC_000001.11 - 154663409 Oct 12, 2022 (156)
65 Genetic variation in the Estonian population NC_000001.10 - 154635885 Oct 11, 2018 (152)
66 gnomAD - Genomes NC_000001.11 - 154663409 Apr 25, 2021 (155)
67 Genome of the Netherlands Release 5 NC_000001.10 - 154635885 Apr 25, 2020 (154)
68 HapMap NC_000001.11 - 154663409 Apr 25, 2020 (154)
69 KOREAN population from KRGDB NC_000001.10 - 154635885 Apr 25, 2020 (154)
70 Korean Genome Project NC_000001.11 - 154663409 Apr 25, 2020 (154)
71 Northern Sweden NC_000001.10 - 154635885 Jul 12, 2019 (153)
72 Qatari NC_000001.10 - 154635885 Apr 25, 2020 (154)
73 SGDP_PRJ NC_000001.10 - 154635885 Apr 25, 2020 (154)
74 Siberian NC_000001.10 - 154635885 Apr 25, 2020 (154)
75 8.3KJPN NC_000001.10 - 154635885 Apr 25, 2021 (155)
76 14KJPN NC_000001.11 - 154663409 Oct 12, 2022 (156)
77 TopMed NC_000001.11 - 154663409 Apr 25, 2021 (155)
78 A Vietnamese Genetic Variation Database NC_000001.10 - 154635885 Jul 12, 2019 (153)
79 ALFA NC_000001.11 - 154663409 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
2391690, ss3895214296 NC_000001.10:154635884:G:A NC_000001.11:154663408:G:A (self)
ss87824911, ss108599863, ss167134428, ss205292984, ss276051451, ss284152766, ss290637201, ss1585064533 NC_000001.9:152902508:G:T NC_000001.11:154663408:G:T (self)
3719904, 1431456, 878693, 2391690, 771056, 958921, 2024572, 514924, 4455108, 434650, ss230732133, ss238380007, ss648414319, ss975683065, ss1068270004, ss1292927740, ss1425979131, ss1918916991, ss1966867682, ss2019974030, ss2147998570, ss2624495062, ss2697971485, ss2761322205, ss2984879337, ss2985525113, ss2987752962, ss3343710770, ss3653648532, ss3655693208, ss3727486191, ss3746808747, ss3826424436, ss3836606835, ss3850007592, ss3895214296, ss5146485801, ss5626592461, ss5832666239, ss5938386354 NC_000001.10:154635884:G:T NC_000001.11:154663408:G:T (self)
5149945, 27067485, 176552, 2030447, 7519402, 31928446, 9474161548, ss2166545668, ss3023744214, ss3646791507, ss3687783538, ss3799810413, ss3842016060, ss3945652446, ss4468322111, ss5244294929, ss5444888191, ss5517624010, ss5673682298, ss5801260574, ss5849109150, ss5910247941 NC_000001.11:154663408:G:T NC_000001.11:154663408:G:T (self)
ss41239218, ss68780540, ss99251191, ss102785653, ss131695640 NT_004487.19:6124526:G:T NC_000001.11:154663408:G:T (self)
ss16384621, ss18070064, ss18243381, ss20433955 NT_079484.1:1085716:G:T NC_000001.11:154663408:G: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 rs10908421

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.post820+afb47a3d