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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.

rs17307398

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chrY:15174113 (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 / T>C / T>G
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.39669 (33938/85554, ALFA)
T=0.2658 (425/1599, 1000G_30x)
T=0.0050 (7/1398, KOREAN) (+ 8 more)
T=0.2660 (328/1233, 1000G)
T=0.389 (348/895, chrY)
T=0.000 (0/296, SGDP_PRJ)
T=0.09 (5/53, Qatari)
T=0.00 (0/48, Vietnamese)
T=0.33 (10/30, Ancient Sardinia)
T=0.00 (0/26, Siberian)
T=0.30 (6/20, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
None
Publications
1 citation
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 85554 T=0.60331 C=0.39669
European Sub 77530 T=0.62654 C=0.37346
African Sub 1786 T=0.2228 C=0.7772
African Others Sub 66 T=0.00 C=1.00
African American Sub 1720 T=0.2314 C=0.7686
Asian Sub 1014 T=0.0059 C=0.9941
East Asian Sub 844 T=0.005 C=0.995
Other Asian Sub 170 T=0.012 C=0.988
Latin American 1 Sub 304 T=0.368 C=0.632
Latin American 2 Sub 1606 T=0.4938 C=0.5062
South Asian Sub 144 T=0.444 C=0.556
Other Sub 3170 T=0.5259 C=0.4741


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
Allele Frequency Aggregator Total Global 85554 T=0.60331 C=0.39669
Allele Frequency Aggregator European Sub 77530 T=0.62654 C=0.37346
Allele Frequency Aggregator Other Sub 3170 T=0.5259 C=0.4741
Allele Frequency Aggregator African Sub 1786 T=0.2228 C=0.7772
Allele Frequency Aggregator Latin American 2 Sub 1606 T=0.4938 C=0.5062
Allele Frequency Aggregator Asian Sub 1014 T=0.0059 C=0.9941
Allele Frequency Aggregator Latin American 1 Sub 304 T=0.368 C=0.632
Allele Frequency Aggregator South Asian Sub 144 T=0.444 C=0.556
1000Genomes_30x Global Study-wide 1599 T=0.2658 C=0.7342
1000Genomes_30x African Sub 458 T=0.033 C=0.967
1000Genomes_30x South Asian Sub 319 T=0.404 C=0.596
1000Genomes_30x Europe Sub 305 T=0.603 C=0.397
1000Genomes_30x East Asian Sub 292 T=0.003 C=0.997
1000Genomes_30x American Sub 225 T=0.427 C=0.573
KOREAN population from KRGDB KOREAN Study-wide 1398 T=0.0050 A=0.0000, C=0.9950, G=0.0000
1000Genomes Global Study-wide 1233 T=0.2660 C=0.7340
1000Genomes African Sub 319 T=0.038 C=0.962
1000Genomes South Asian Sub 260 T=0.388 C=0.612
1000Genomes East Asian Sub 244 T=0.004 C=0.996
1000Genomes Europe Sub 240 T=0.583 C=0.417
1000Genomes American Sub 170 T=0.435 C=0.565
chrY_custom_capture Global Study-wide 895 T=0.389 C=0.611
chrY_custom_capture AFP Sub 0 T=0 C=0
chrY_custom_capture AHG Sub 0 T=0 C=0
chrY_custom_capture ASC Sub 0 T=0 C=0
chrY_custom_capture ASE Sub 0 T=0 C=0
chrY_custom_capture AUS Sub 0 T=0 C=0
chrY_custom_capture BRI Sub 0 T=0 C=0
chrY_custom_capture ENV Sub 0 T=0 C=0
chrY_custom_capture ESC Sub 0 T=0 C=0
chrY_custom_capture ESE Sub 0 T=0 C=0
chrY_custom_capture ESW Sub 0 T=0 C=0
chrY_custom_capture MEX Sub 0 T=0 C=0
chrY_custom_capture MNE Sub 0 T=0 C=0
chrY_custom_capture SCA Sub 0 T=0 C=0
SGDP_PRJ Global Study-wide 296 T=0.000 C=1.000
Qatari Global Study-wide 53 T=0.09 C=0.91
A Vietnamese Genetic Variation Database Global Study-wide 48 T=0.00 C=1.00
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 30 T=0.33 C=0.67
Siberian Global Study-wide 26 T=0.00 C=1.00
The Danish reference pan genome Danish Study-wide 20 T=0.30 C=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 Y NC_000024.10:g.15174113T>A
GRCh38.p14 chr Y NC_000024.10:g.15174113T>C
GRCh38.p14 chr Y NC_000024.10:g.15174113T>G
GRCh37.p13 chr Y NC_000024.9:g.17285993T>A
GRCh37.p13 chr Y NC_000024.9:g.17285993T>C
GRCh37.p13 chr Y NC_000024.9:g.17285993T>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 T= A C G
GRCh38.p14 chr Y NC_000024.10:g.15174113= NC_000024.10:g.15174113T>A NC_000024.10:g.15174113T>C NC_000024.10:g.15174113T>G
GRCh37.p13 chr Y NC_000024.9:g.17285993= NC_000024.9:g.17285993T>A NC_000024.9:g.17285993T>C NC_000024.9:g.17285993T>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#.

81 SubSNP, 11 Frequency submissions
No Submitter Submission ID Date (Build)
1 PERLEGEN ss24723896 Sep 20, 2004 (123)
2 ILLUMINA ss75271583 Dec 06, 2007 (129)
3 BGI ss105778396 Feb 04, 2009 (130)
4 ILLUMINA-UK ss115581977 Feb 04, 2009 (130)
5 GMI ss157860270 Dec 01, 2009 (131)
6 ILLUMINA ss160438921 Dec 01, 2009 (131)
7 COMPLETE_GENOMICS ss162982834 Jul 04, 2010 (132)
8 ILLUMINA ss172806190 Jul 04, 2010 (132)
9 BUSHMAN ss204418294 Jul 04, 2010 (132)
10 GMI ss283922835 May 04, 2012 (137)
11 ILLUMINA ss480226187 May 04, 2012 (137)
12 ILLUMINA ss480236823 May 04, 2012 (137)
13 ILLUMINA ss480971902 Sep 08, 2015 (146)
14 ILLUMINA ss484911094 May 04, 2012 (137)
15 ILLUMINA ss536963432 Jul 19, 2016 (147)
16 TISHKOFF ss567114955 Apr 25, 2013 (138)
17 SSMP ss663098161 Apr 25, 2013 (138)
18 ILLUMINA ss778459632 Sep 08, 2015 (146)
19 ILLUMINA ss782901861 Sep 08, 2015 (146)
20 ILLUMINA ss783865202 Sep 08, 2015 (146)
21 CDBUSTAMANTE ss825685291 Aug 21, 2014 (142)
22 ILLUMINA ss832156667 Sep 08, 2015 (146)
23 ILLUMINA ss833915321 Sep 08, 2015 (146)
24 JOBLING_UOL ss1399959985 Apr 01, 2015 (144)
25 DDI ss1432160491 Apr 01, 2015 (144)
26 1000GENOMES ss1556761594 Apr 01, 2015 (144)
27 EVA_GENOME_DK ss1583556074 Apr 01, 2015 (144)
28 ILLUMINA ss1752814656 Sep 08, 2015 (146)
29 WEILL_CORNELL_DGM ss1939862266 Feb 12, 2016 (147)
30 ILLUMINA ss1945969295 Feb 12, 2016 (147)
31 ILLUMINA ss1958177962 Feb 12, 2016 (147)
32 ILLUMINA ss1958177963 Feb 12, 2016 (147)
33 ILLUMINA ss2094838746 Dec 20, 2016 (150)
34 ILLUMINA ss2095229794 Dec 20, 2016 (150)
35 USC_VALOUEV ss2159354685 Dec 20, 2016 (150)
36 HUMAN_LONGEVITY ss2321433919 Dec 20, 2016 (150)
37 SYSTEMSBIOZJU ss2629805011 Nov 08, 2017 (151)
38 ILLUMINA ss2634994288 Nov 08, 2017 (151)
39 GRF ss2710439645 Nov 08, 2017 (151)
40 SWEGEN ss3020953437 Nov 08, 2017 (151)
41 ILLUMINA ss3023053956 Nov 08, 2017 (151)
42 ILLUMINA ss3023053957 Nov 08, 2017 (151)
43 HUMGEN ss3029949331 Nov 08, 2017 (151)
44 ILLUMINA ss3626005665 Oct 12, 2018 (152)
45 ILLUMINA ss3630504656 Oct 12, 2018 (152)
46 ILLUMINA ss3632877183 Oct 12, 2018 (152)
47 ILLUMINA ss3633570835 Oct 12, 2018 (152)
48 ILLUMINA ss3634301184 Oct 12, 2018 (152)
49 ILLUMINA ss3635264985 Oct 12, 2018 (152)
50 ILLUMINA ss3635977995 Oct 12, 2018 (152)
51 ILLUMINA ss3637015146 Oct 12, 2018 (152)
52 ILLUMINA ss3637731730 Oct 12, 2018 (152)
53 ILLUMINA ss3638887001 Oct 12, 2018 (152)
54 ILLUMINA ss3640972473 Oct 12, 2018 (152)
55 ILLUMINA ss3641266182 Oct 12, 2018 (152)
56 ILLUMINA ss3641565105 Oct 12, 2018 (152)
57 ILLUMINA ss3643809701 Oct 12, 2018 (152)
58 ILLUMINA ss3645021635 Oct 12, 2018 (152)
59 ILLUMINA ss3653612511 Oct 12, 2018 (152)
60 ILLUMINA ss3653612512 Oct 12, 2018 (152)
61 ILLUMINA ss3726713846 Jul 14, 2019 (153)
62 ILLUMINA ss3744336468 Jul 14, 2019 (153)
63 ILLUMINA ss3745564998 Jul 14, 2019 (153)
64 ILLUMINA ss3773056605 Jul 14, 2019 (153)
65 PACBIO ss3788976297 Jul 14, 2019 (153)
66 PACBIO ss3793846740 Jul 14, 2019 (153)
67 PACBIO ss3798731233 Jul 14, 2019 (153)
68 KHV_HUMAN_GENOMES ss3823536928 Jul 14, 2019 (153)
69 EVA ss3836374110 Apr 27, 2020 (154)
70 SGDP_PRJ ss3892723632 Apr 27, 2020 (154)
71 KRGDB ss3943516731 Apr 27, 2020 (154)
72 EVA ss3984772464 Apr 27, 2021 (155)
73 EVA ss3985993752 Apr 27, 2021 (155)
74 ESTONIANBIOCENTRE ss5237682985 Oct 17, 2022 (156)
75 EVA ss5316103925 Oct 17, 2022 (156)
76 1000G_HIGH_COVERAGE ss5623835565 Oct 17, 2022 (156)
77 SANFORD_IMAGENETICS ss5666139982 Oct 17, 2022 (156)
78 YY_MCH ss5819517479 Oct 17, 2022 (156)
79 EVA ss5848242597 Oct 17, 2022 (156)
80 EVA ss5857247623 Oct 17, 2022 (156)
81 EVA ss5979925465 Oct 17, 2022 (156)
82 1000Genomes NC_000024.9 - 17285993 Oct 12, 2018 (152)
83 1000Genomes_30x NC_000024.10 - 15174113 Oct 17, 2022 (156)
84 chrY_custom_capture NC_000024.9 - 17285993 Apr 27, 2020 (154)
85 The Danish reference pan genome NC_000024.9 - 17285993 Apr 27, 2020 (154)
86 KOREAN population from KRGDB NC_000024.9 - 17285993 Apr 27, 2020 (154)
87 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000024.9 - 17285993 Apr 27, 2021 (155)
88 Qatari NC_000024.9 - 17285993 Apr 27, 2020 (154)
89 SGDP_PRJ NC_000024.9 - 17285993 Apr 27, 2020 (154)
90 Siberian NC_000024.9 - 17285993 Apr 27, 2020 (154)
91 A Vietnamese Genetic Variation Database NC_000024.9 - 17285993 Jul 14, 2019 (153)
92 ALFA NC_000024.10 - 15174113 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
50694125, ss3943516731 NC_000024.9:17285992:T:A NC_000024.10:15174112:T:A (self)
ss162982834, ss204418294, ss283922835, ss480226187, ss3643809701 NC_000024.8:15795386:T:C NC_000024.10:15174112:T:C (self)
84714582, 7260, 9721011, 50694125, 1219679, 21904188, 44740612, 11871039, 10243356, ss480236823, ss480971902, ss484911094, ss536963432, ss567114955, ss663098161, ss778459632, ss782901861, ss783865202, ss825685291, ss832156667, ss833915321, ss1399959985, ss1432160491, ss1556761594, ss1583556074, ss1752814656, ss1939862266, ss1945969295, ss1958177962, ss1958177963, ss2094838746, ss2095229794, ss2159354685, ss2629805011, ss2634994288, ss2710439645, ss3020953437, ss3023053956, ss3023053957, ss3029949331, ss3626005665, ss3630504656, ss3632877183, ss3633570835, ss3634301184, ss3635264985, ss3635977995, ss3637015146, ss3637731730, ss3638887001, ss3640972473, ss3641266182, ss3641565105, ss3645021635, ss3653612511, ss3653612512, ss3744336468, ss3745564998, ss3773056605, ss3788976297, ss3793846740, ss3798731233, ss3836374110, ss3892723632, ss3943516731, ss3984772464, ss3985993752, ss5237682985, ss5316103925, ss5666139982, ss5848242597, ss5979925465 NC_000024.9:17285992:T:C NC_000024.10:15174112:T:C (self)
111361500, 1284105379, ss2321433919, ss3726713846, ss3823536928, ss5623835565, ss5819517479, ss5857247623 NC_000024.10:15174112:T:C NC_000024.10:15174112:T:C (self)
ss24723896, ss75271583, ss105778396, ss115581977, ss157860270, ss160438921, ss172806190 NT_011875.12:3487414:T:C NC_000024.10:15174112:T:C (self)
50694125, ss3943516731 NC_000024.9:17285992:T:G NC_000024.10:15174112:T:G (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

1 citation for rs17307398
PMID Title Author Year Journal
22649659 Individual Genome of the Russian Male: SNP Calling and a de novo Assembly of Unmapped Reads. Chekanov NN et al. 2010 Acta naturae
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