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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.

rs2045088

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr17:44405865 (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
T>A
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.497503 (131684/264690, TOPMED)
A=0.497365 (69637/140012, GnomAD)
T=0.48857 (13806/28258, 14KJPN) (+ 15 more)
T=0.45093 (8538/18934, ALFA)
T=0.48622 (8149/16760, 8.3KJPN)
A=0.4471 (2863/6404, 1000G_30x)
A=0.4457 (2232/5008, 1000G)
T=0.3765 (1451/3854, ALSPAC)
T=0.3668 (1360/3708, TWINSUK)
T=0.4495 (1317/2930, KOREAN)
T=0.4405 (807/1832, Korea1K)
T=0.435 (434/998, GoNL)
T=0.422 (253/600, NorthernSweden)
A=0.013 (7/534, MGP)
T=0.296 (118/398, SGDP_PRJ)
T=0.440 (95/216, Qatari)
A=0.42 (17/40, GENOME_DK)
T=0.33 (13/40, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
GPATCH8 : Intron 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 18934 T=0.45093 A=0.54907
European Sub 14318 T=0.39607 A=0.60393
African Sub 2954 T=0.7221 A=0.2779
African Others Sub 114 T=0.772 A=0.228
African American Sub 2840 T=0.7201 A=0.2799
Asian Sub 112 T=0.446 A=0.554
East Asian Sub 86 T=0.43 A=0.57
Other Asian Sub 26 T=0.50 A=0.50
Latin American 1 Sub 146 T=0.479 A=0.521
Latin American 2 Sub 610 T=0.402 A=0.598
South Asian Sub 98 T=0.55 A=0.45
Other Sub 696 T=0.453 A=0.547


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 T=0.497503 A=0.502497
gnomAD - Genomes Global Study-wide 140012 T=0.502635 A=0.497365
gnomAD - Genomes European Sub 75816 T=0.40142 A=0.59858
gnomAD - Genomes African Sub 41958 T=0.72432 A=0.27568
gnomAD - Genomes American Sub 13640 T=0.41246 A=0.58754
gnomAD - Genomes Ashkenazi Jewish Sub 3322 T=0.4028 A=0.5972
gnomAD - Genomes East Asian Sub 3124 T=0.5054 A=0.4946
gnomAD - Genomes Other Sub 2152 T=0.4679 A=0.5321
14KJPN JAPANESE Study-wide 28258 T=0.48857 A=0.51143
Allele Frequency Aggregator Total Global 18934 T=0.45093 A=0.54907
Allele Frequency Aggregator European Sub 14318 T=0.39607 A=0.60393
Allele Frequency Aggregator African Sub 2954 T=0.7221 A=0.2779
Allele Frequency Aggregator Other Sub 696 T=0.453 A=0.547
Allele Frequency Aggregator Latin American 2 Sub 610 T=0.402 A=0.598
Allele Frequency Aggregator Latin American 1 Sub 146 T=0.479 A=0.521
Allele Frequency Aggregator Asian Sub 112 T=0.446 A=0.554
Allele Frequency Aggregator South Asian Sub 98 T=0.55 A=0.45
8.3KJPN JAPANESE Study-wide 16760 T=0.48622 A=0.51378
1000Genomes_30x Global Study-wide 6404 T=0.5529 A=0.4471
1000Genomes_30x African Sub 1786 T=0.7648 A=0.2352
1000Genomes_30x Europe Sub 1266 T=0.4013 A=0.5987
1000Genomes_30x South Asian Sub 1202 T=0.5666 A=0.4334
1000Genomes_30x East Asian Sub 1170 T=0.4991 A=0.5009
1000Genomes_30x American Sub 980 T=0.410 A=0.590
1000Genomes Global Study-wide 5008 T=0.5543 A=0.4457
1000Genomes African Sub 1322 T=0.7670 A=0.2330
1000Genomes East Asian Sub 1008 T=0.5030 A=0.4970
1000Genomes Europe Sub 1006 T=0.3976 A=0.6024
1000Genomes South Asian Sub 978 T=0.577 A=0.423
1000Genomes American Sub 694 T=0.419 A=0.581
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.3765 A=0.6235
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.3668 A=0.6332
KOREAN population from KRGDB KOREAN Study-wide 2930 T=0.4495 A=0.5505
Korean Genome Project KOREAN Study-wide 1832 T=0.4405 A=0.5595
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.435 A=0.565
Northern Sweden ACPOP Study-wide 600 T=0.422 A=0.578
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 T=0.987 A=0.013
SGDP_PRJ Global Study-wide 398 T=0.296 A=0.704
Qatari Global Study-wide 216 T=0.440 A=0.560
The Danish reference pan genome Danish Study-wide 40 T=0.57 A=0.42
Siberian Global Study-wide 40 T=0.33 A=0.68
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 17 NC_000017.11:g.44405865T>A
GRCh37.p13 chr 17 NC_000017.10:g.42483233T>A
GPATCH8 RefSeqGene NG_041943.1:g.102738A>T
Gene: GPATCH8, G-patch domain containing 8 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
GPATCH8 transcript variant 1 NM_001002909.4:c.623+56A>T N/A Intron Variant
GPATCH8 transcript variant 2 NM_001304939.2:c.548+56A>T N/A Intron Variant
GPATCH8 transcript variant 3 NM_001304940.2:c.389+56A>T N/A Intron Variant
GPATCH8 transcript variant 4 NM_001304941.2:c.389+56A>T N/A Intron Variant
GPATCH8 transcript variant 5 NM_001304942.2:c.389+56A>T N/A Intron Variant
GPATCH8 transcript variant 6 NM_001304943.2:c.389+56A>T N/A Intron Variant
GPATCH8 transcript variant X1 XM_011524557.2:c.710+56A>T N/A Intron Variant
GPATCH8 transcript variant X2 XM_011524558.3:c.476+56A>T N/A Intron Variant
GPATCH8 transcript variant X3 XM_011524559.3:c.476+56A>T N/A Intron Variant
GPATCH8 transcript variant X4 XM_011524561.3:c.476+56A>T N/A Intron Variant
GPATCH8 transcript variant X7 XM_017024373.2:c.476+56A>T N/A Intron Variant
GPATCH8 transcript variant X5 XM_047435672.1:c.476+56A>T N/A Intron Variant
GPATCH8 transcript variant X6 XM_047435673.1:c.476+56A>T N/A Intron Variant
GPATCH8 transcript variant X8 XM_047435674.1:c.389+56A>T N/A Intron 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 T= A
GRCh38.p14 chr 17 NC_000017.11:g.44405865= NC_000017.11:g.44405865T>A
GRCh37.p13 chr 17 NC_000017.10:g.42483233= NC_000017.10:g.42483233T>A
GPATCH8 RefSeqGene NG_041943.1:g.102738= NG_041943.1:g.102738A>T
GPATCH8 transcript variant 1 NM_001002909.2:c.623+56= NM_001002909.2:c.623+56A>T
GPATCH8 transcript variant 1 NM_001002909.4:c.623+56= NM_001002909.4:c.623+56A>T
GPATCH8 transcript variant 2 NM_001304939.2:c.548+56= NM_001304939.2:c.548+56A>T
GPATCH8 transcript variant 3 NM_001304940.2:c.389+56= NM_001304940.2:c.389+56A>T
GPATCH8 transcript variant 4 NM_001304941.2:c.389+56= NM_001304941.2:c.389+56A>T
GPATCH8 transcript variant 5 NM_001304942.2:c.389+56= NM_001304942.2:c.389+56A>T
GPATCH8 transcript variant 6 NM_001304943.2:c.389+56= NM_001304943.2:c.389+56A>T
GPATCH8 transcript variant X1 XM_011524557.2:c.710+56= XM_011524557.2:c.710+56A>T
GPATCH8 transcript variant X2 XM_011524558.3:c.476+56= XM_011524558.3:c.476+56A>T
GPATCH8 transcript variant X3 XM_011524559.3:c.476+56= XM_011524559.3:c.476+56A>T
GPATCH8 transcript variant X4 XM_011524561.3:c.476+56= XM_011524561.3:c.476+56A>T
GPATCH8 transcript variant X7 XM_017024373.2:c.476+56= XM_017024373.2:c.476+56A>T
GPATCH8 transcript variant X5 XM_047435672.1:c.476+56= XM_047435672.1:c.476+56A>T
GPATCH8 transcript variant X6 XM_047435673.1:c.476+56= XM_047435673.1:c.476+56A>T
GPATCH8 transcript variant X8 XM_047435674.1:c.389+56= XM_047435674.1:c.389+56A>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#.

72 SubSNP, 18 Frequency submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss2954999 Apr 12, 2001 (94)
2 SC_JCM ss6268574 Feb 20, 2003 (111)
3 ABI ss40821702 Mar 14, 2006 (126)
4 HGSV ss77496250 Dec 07, 2007 (129)
5 BCMHGSC_JDW ss90592714 Mar 24, 2008 (129)
6 BGI ss103347041 Dec 01, 2009 (131)
7 1000GENOMES ss109774659 Jan 24, 2009 (130)
8 ILLUMINA-UK ss118058842 Dec 01, 2009 (131)
9 ENSEMBL ss137078213 Dec 01, 2009 (131)
10 GMI ss158046130 Dec 01, 2009 (131)
11 BCM-HGSC-SUB ss208022045 Jul 04, 2010 (132)
12 1000GENOMES ss227553279 Jul 14, 2010 (132)
13 1000GENOMES ss237247120 Jul 15, 2010 (132)
14 1000GENOMES ss243544677 Jul 15, 2010 (132)
15 BL ss255646699 May 09, 2011 (134)
16 GMI ss282770482 May 04, 2012 (137)
17 PJP ss292053734 May 09, 2011 (134)
18 SSMP ss661083314 Apr 25, 2013 (138)
19 EVA-GONL ss993119999 Aug 21, 2014 (142)
20 JMKIDD_LAB ss1081066754 Aug 21, 2014 (142)
21 1000GENOMES ss1358706583 Aug 21, 2014 (142)
22 DDI ss1428036987 Apr 01, 2015 (144)
23 EVA_GENOME_DK ss1578161554 Apr 01, 2015 (144)
24 EVA_UK10K_ALSPAC ss1635677847 Apr 01, 2015 (144)
25 EVA_UK10K_TWINSUK ss1678671880 Apr 01, 2015 (144)
26 EVA_DECODE ss1697163368 Apr 01, 2015 (144)
27 EVA_MGP ss1711462759 Apr 01, 2015 (144)
28 WEILL_CORNELL_DGM ss1936580485 Feb 12, 2016 (147)
29 JJLAB ss2029066765 Sep 14, 2016 (149)
30 USC_VALOUEV ss2157538561 Dec 20, 2016 (150)
31 HUMAN_LONGEVITY ss2216946509 Dec 20, 2016 (150)
32 SYSTEMSBIOZJU ss2629029435 Nov 08, 2017 (151)
33 GRF ss2702100966 Nov 08, 2017 (151)
34 GNOMAD ss2950023219 Nov 08, 2017 (151)
35 SWEGEN ss3015556031 Nov 08, 2017 (151)
36 BIOINF_KMB_FNS_UNIBA ss3028353627 Nov 08, 2017 (151)
37 CSHL ss3351751831 Nov 08, 2017 (151)
38 OMUKHERJEE_ADBS ss3646512130 Oct 12, 2018 (152)
39 EVA_DECODE ss3700491798 Jul 13, 2019 (153)
40 ACPOP ss3742036123 Jul 13, 2019 (153)
41 EVA ss3754681890 Jul 13, 2019 (153)
42 PACBIO ss3788207288 Jul 13, 2019 (153)
43 PACBIO ss3793163842 Jul 13, 2019 (153)
44 PACBIO ss3798049684 Jul 13, 2019 (153)
45 KHV_HUMAN_GENOMES ss3819951041 Jul 13, 2019 (153)
46 EVA ss3834873527 Apr 27, 2020 (154)
47 SGDP_PRJ ss3885775413 Apr 27, 2020 (154)
48 KRGDB ss3935469093 Apr 27, 2020 (154)
49 KOGIC ss3978873760 Apr 27, 2020 (154)
50 FSA-LAB ss3984116775 Apr 27, 2021 (155)
51 EVA ss3986729732 Apr 27, 2021 (155)
52 TOPMED ss5036446361 Apr 27, 2021 (155)
53 TOMMO_GENOMICS ss5222478845 Apr 27, 2021 (155)
54 EVA ss5237239471 Apr 27, 2021 (155)
55 1000G_HIGH_COVERAGE ss5303179539 Oct 16, 2022 (156)
56 HUGCELL_USP ss5496230228 Oct 16, 2022 (156)
57 EVA ss5511769434 Oct 16, 2022 (156)
58 1000G_HIGH_COVERAGE ss5606921509 Oct 16, 2022 (156)
59 EVA ss5623971476 Oct 16, 2022 (156)
60 EVA ss5624073147 Oct 16, 2022 (156)
61 SANFORD_IMAGENETICS ss5660128441 Oct 16, 2022 (156)
62 TOMMO_GENOMICS ss5778710910 Oct 16, 2022 (156)
63 EVA ss5800209232 Oct 16, 2022 (156)
64 YY_MCH ss5816553294 Oct 16, 2022 (156)
65 EVA ss5834001080 Oct 16, 2022 (156)
66 EVA ss5848450723 Oct 16, 2022 (156)
67 EVA ss5851813158 Oct 16, 2022 (156)
68 EVA ss5914009633 Oct 16, 2022 (156)
69 EVA ss5936567882 Oct 16, 2022 (156)
70 EVA ss5951521426 Oct 16, 2022 (156)
71 EVA ss5980968277 Oct 16, 2022 (156)
72 EVA ss5981301794 Oct 16, 2022 (156)
73 1000Genomes NC_000017.10 - 42483233 Oct 12, 2018 (152)
74 1000Genomes_30x NC_000017.11 - 44405865 Oct 16, 2022 (156)
75 The Avon Longitudinal Study of Parents and Children NC_000017.10 - 42483233 Oct 12, 2018 (152)
76 The Danish reference pan genome NC_000017.10 - 42483233 Apr 27, 2020 (154)
77 gnomAD - Genomes NC_000017.11 - 44405865 Apr 27, 2021 (155)
78 Genome of the Netherlands Release 5 NC_000017.10 - 42483233 Apr 27, 2020 (154)
79 KOREAN population from KRGDB NC_000017.10 - 42483233 Apr 27, 2020 (154)
80 Korean Genome Project NC_000017.11 - 44405865 Apr 27, 2020 (154)
81 Medical Genome Project healthy controls from Spanish population NC_000017.10 - 42483233 Apr 27, 2020 (154)
82 Northern Sweden NC_000017.10 - 42483233 Jul 13, 2019 (153)
83 Qatari NC_000017.10 - 42483233 Apr 27, 2020 (154)
84 SGDP_PRJ NC_000017.10 - 42483233 Apr 27, 2020 (154)
85 Siberian NC_000017.10 - 42483233 Apr 27, 2020 (154)
86 8.3KJPN NC_000017.10 - 42483233 Apr 27, 2021 (155)
87 14KJPN NC_000017.11 - 44405865 Oct 16, 2022 (156)
88 TopMed NC_000017.11 - 44405865 Apr 27, 2021 (155)
89 UK 10K study - Twins NC_000017.10 - 42483233 Oct 12, 2018 (152)
90 ALFA NC_000017.11 - 44405865 Apr 27, 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
ss77496250, ss90592714, ss109774659, ss118058842, ss208022045, ss255646699, ss282770482, ss292053734, ss1697163368 NC_000017.9:39838758:T:A NC_000017.11:44405864:T:A (self)
71950222, 39876459, 4363782, 17771373, 42646487, 578519, 15320988, 18622407, 37792393, 10054915, 80448152, 39876459, ss227553279, ss237247120, ss243544677, ss661083314, ss993119999, ss1081066754, ss1358706583, ss1428036987, ss1578161554, ss1635677847, ss1678671880, ss1711462759, ss1936580485, ss2029066765, ss2157538561, ss2629029435, ss2702100966, ss2950023219, ss3015556031, ss3351751831, ss3646512130, ss3742036123, ss3754681890, ss3788207288, ss3793163842, ss3798049684, ss3834873527, ss3885775413, ss3935469093, ss3984116775, ss3986729732, ss5222478845, ss5511769434, ss5623971476, ss5624073147, ss5660128441, ss5800209232, ss5834001080, ss5848450723, ss5936567882, ss5951521426, ss5980968277, ss5981301794 NC_000017.10:42483232:T:A NC_000017.11:44405864:T:A (self)
94447444, 507638104, 35251761, 112548014, 251992023, 2961812814, ss2216946509, ss3028353627, ss3700491798, ss3819951041, ss3978873760, ss5036446361, ss5237239471, ss5303179539, ss5496230228, ss5606921509, ss5778710910, ss5816553294, ss5851813158, ss5914009633 NC_000017.11:44405864:T:A NC_000017.11:44405864:T:A (self)
ss2954999, ss6268574, ss40821702, ss103347041, ss137078213, ss158046130 NT_010783.15:7757384:T:A NC_000017.11:44405864:T: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 rs2045088

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