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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.

rs13447352

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chrY:20587967 (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
A>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.09480 (3477/36678, ALFA)
C=0.04253 (1293/30404, GnomAD)
C=0.0563 (90/1599, 1000G_30x) (+ 7 more)
C=0.0616 (76/1233, 1000G)
C=0.074 (66/896, chrY)
C=0.365 (298/816, Daghestan)
C=0.034 (18/534, MGP)
A=0.36 (19/53, Qatari)
A=0.00 (0/48, SGDP_PRJ)
C=0.0 (0/4, Ancient Sardinia)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
EIF1AY : Intron Variant
Publications
4 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 36678 A=0.90520 C=0.09480
European Sub 33176 A=0.90578 C=0.09422
African Sub 466 A=0.955 C=0.045
African Others Sub 16 A=1.00 C=0.00
African American Sub 450 A=0.953 C=0.047
Asian Sub 44 A=0.93 C=0.07
East Asian Sub 34 A=0.91 C=0.09
Other Asian Sub 10 A=1.0 C=0.0
Latin American 1 Sub 4 A=0.5 C=0.5
Latin American 2 Sub 16 A=0.75 C=0.25
South Asian Sub 6 A=1.0 C=0.0
Other Sub 2966 A=0.8918 C=0.1082


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 36678 A=0.90520 C=0.09480
Allele Frequency Aggregator European Sub 33176 A=0.90578 C=0.09422
Allele Frequency Aggregator Other Sub 2966 A=0.8918 C=0.1082
Allele Frequency Aggregator African Sub 466 A=0.955 C=0.045
Allele Frequency Aggregator Asian Sub 44 A=0.93 C=0.07
Allele Frequency Aggregator Latin American 2 Sub 16 A=0.75 C=0.25
Allele Frequency Aggregator South Asian Sub 6 A=1.0 C=0.0
Allele Frequency Aggregator Latin American 1 Sub 4 A=0.5 C=0.5
gnomAD - Genomes Global Study-wide 30404 A=0.95747 C=0.04253
gnomAD - Genomes European Sub 16461 A=0.96191 C=0.03809
gnomAD - Genomes African Sub 8640 A=0.9880 C=0.0120
gnomAD - Genomes American Sub 3315 A=0.9231 C=0.0769
gnomAD - Genomes East Asian Sub 787 A=1.000 C=0.000
gnomAD - Genomes Ashkenazi Jewish Sub 740 A=0.642 C=0.358
gnomAD - Genomes Other Sub 461 A=0.909 C=0.091
1000Genomes_30x Global Study-wide 1599 A=0.9437 C=0.0563
1000Genomes_30x African Sub 458 A=1.000 C=0.000
1000Genomes_30x South Asian Sub 319 A=0.871 C=0.129
1000Genomes_30x Europe Sub 305 A=0.898 C=0.102
1000Genomes_30x East Asian Sub 292 A=1.000 C=0.000
1000Genomes_30x American Sub 225 A=0.920 C=0.080
1000Genomes Global Study-wide 1233 A=0.9384 C=0.0616
1000Genomes African Sub 319 A=1.000 C=0.000
1000Genomes South Asian Sub 260 A=0.865 C=0.135
1000Genomes East Asian Sub 244 A=1.000 C=0.000
1000Genomes Europe Sub 240 A=0.887 C=0.113
1000Genomes American Sub 170 A=0.918 C=0.082
chrY_custom_capture Global Study-wide 896 A=0.926 C=0.074
chrY_custom_capture AFP Sub 0 A=0 C=0
chrY_custom_capture AHG Sub 0 A=0 C=0
chrY_custom_capture ASC Sub 0 A=0 C=0
chrY_custom_capture ASE Sub 0 A=0 C=0
chrY_custom_capture AUS Sub 0 A=0 C=0
chrY_custom_capture BRI Sub 0 A=0 C=0
chrY_custom_capture ENV Sub 0 A=0 C=0
chrY_custom_capture ESC Sub 0 A=0 C=0
chrY_custom_capture ESE Sub 0 A=0 C=0
chrY_custom_capture ESW Sub 0 A=0 C=0
chrY_custom_capture MEX Sub 0 A=0 C=0
chrY_custom_capture MNE Sub 0 A=0 C=0
chrY_custom_capture SCA Sub 0 A=0 C=0
Genome-wide autozygosity in Daghestan Global Study-wide 816 A=0.635 C=0.365
Genome-wide autozygosity in Daghestan Daghestan Sub 308 A=0.390 C=0.610
Genome-wide autozygosity in Daghestan Near_East Sub 144 A=0.681 C=0.319
Genome-wide autozygosity in Daghestan Central Asia Sub 122 A=0.852 C=0.148
Genome-wide autozygosity in Daghestan Europe Sub 108 A=0.889 C=0.111
Genome-wide autozygosity in Daghestan South Asian Sub 98 A=0.82 C=0.18
Genome-wide autozygosity in Daghestan Caucasus Sub 36 A=0.56 C=0.44
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 A=0.966 C=0.034
Qatari Global Study-wide 53 A=0.36 C=0.64
SGDP_PRJ Global Study-wide 48 A=0.00 C=1.00
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 4 A=1.0 C=0.0
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.20587967A>C
GRCh37.p13 chr Y NC_000024.9:g.22749853A>C
Gene: EIF1AY, eukaryotic translation initiation factor 1A Y-linked (plus strand)
Molecule type Change Amino acid[Codon] SO Term
EIF1AY transcript variant 2 NM_001278612.2:c.205-57A>C N/A Intron Variant
EIF1AY transcript variant 1 NM_004681.4:c.256-57A>C 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 A= C
GRCh38.p14 chr Y NC_000024.10:g.20587967= NC_000024.10:g.20587967A>C
GRCh37.p13 chr Y NC_000024.9:g.22749853= NC_000024.9:g.22749853A>C
EIF1AY transcript variant 2 NM_001278612.1:c.205-57= NM_001278612.1:c.205-57A>C
EIF1AY transcript variant 2 NM_001278612.2:c.205-57= NM_001278612.2:c.205-57A>C
EIF1AY transcript variant 1 NM_004681.3:c.256-57= NM_004681.3:c.256-57A>C
EIF1AY transcript variant 1 NM_004681.4:c.256-57= NM_004681.4:c.256-57A>C
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, 10 Frequency submissions
No Submitter Submission ID Date (Build)
1 OEFNER ss23129223 Apr 05, 2004 (121)
2 PERLEGEN ss24726420 Sep 20, 2004 (123)
3 PAGE ss50392487 Mar 14, 2006 (126)
4 ILLUMINA ss75013293 Dec 07, 2007 (129)
5 ILLUMINA ss172428632 Jul 04, 2010 (132)
6 EXOME_CHIP ss491581257 May 04, 2012 (137)
7 SSMP ss663101710 Apr 25, 2013 (138)
8 ILLUMINA ss780681822 Aug 21, 2014 (142)
9 ILLUMINA ss783355154 Aug 21, 2014 (142)
10 HAMMER_LAB ss1397805102 Sep 08, 2015 (146)
11 JOBLING_UOL ss1399965419 Apr 01, 2015 (144)
12 DDI ss1432162008 Apr 01, 2015 (144)
13 1000GENOMES ss1556781709 Apr 01, 2015 (144)
14 EVA_MGP ss1711594193 Apr 01, 2015 (144)
15 ILLUMINA ss1752815127 Sep 08, 2015 (146)
16 ILLUMINA ss1917716486 Feb 12, 2016 (147)
17 WEILL_CORNELL_DGM ss1939864921 Feb 12, 2016 (147)
18 ILLUMINA ss1945970323 Feb 12, 2016 (147)
19 ILLUMINA ss1958181598 Feb 12, 2016 (147)
20 ILLUMINA ss1958181599 Feb 12, 2016 (147)
21 ILLUMINA ss2094839181 Dec 20, 2016 (150)
22 ILLUMINA ss2095230185 Dec 20, 2016 (150)
23 HUMAN_LONGEVITY ss2321485323 Dec 20, 2016 (150)
24 ILLUMINA ss2635204651 Nov 08, 2017 (151)
25 ILLUMINA ss2711191767 Nov 08, 2017 (151)
26 AFFY ss2985494935 Nov 08, 2017 (151)
27 SWEGEN ss3020974519 Nov 08, 2017 (151)
28 ILLUMINA ss3023055268 Nov 08, 2017 (151)
29 ILLUMINA ss3023055269 Nov 08, 2017 (151)
30 HUMGEN ss3029951912 Nov 08, 2017 (151)
31 ILLUMINA ss3630505235 Oct 12, 2018 (152)
32 ILLUMINA ss3635265380 Oct 12, 2018 (152)
33 ILLUMINA ss3638887507 Oct 12, 2018 (152)
34 ILLUMINA ss3640972870 Oct 12, 2018 (152)
35 ILLUMINA ss3643810234 Oct 12, 2018 (152)
36 ILLUMINA ss3645022138 Oct 12, 2018 (152)
37 ILLUMINA ss3653613908 Oct 12, 2018 (152)
38 ILLUMINA ss3653613909 Oct 12, 2018 (152)
39 ILLUMINA ss3653613910 Oct 12, 2018 (152)
40 ILLUMINA ss3654261662 Oct 12, 2018 (152)
41 ILLUMINA ss3726714778 Jul 14, 2019 (153)
42 ILLUMINA ss3744602736 Jul 14, 2019 (153)
43 ILLUMINA ss3745565378 Jul 14, 2019 (153)
44 ILLUMINA ss3773056983 Jul 14, 2019 (153)
45 PACBIO ss3788977743 Jul 14, 2019 (153)
46 PACBIO ss3793849517 Jul 14, 2019 (153)
47 PACBIO ss3798734213 Jul 14, 2019 (153)
48 KHV_HUMAN_GENOMES ss3823540043 Jul 14, 2019 (153)
49 EVA ss3836375766 Apr 27, 2020 (154)
50 SGDP_PRJ ss3892774749 Apr 27, 2020 (154)
51 FSA-LAB ss3984446710 Apr 27, 2021 (155)
52 EVA ss3984773346 Apr 27, 2021 (155)
53 EVA ss3986004410 Apr 27, 2021 (155)
54 EVA ss3986888994 Apr 27, 2021 (155)
55 GNOMAD ss4126292037 Apr 27, 2021 (155)
56 ESTONIANBIOCENTRE ss5237686024 Oct 13, 2022 (156)
57 EVA ss5316104173 Oct 13, 2022 (156)
58 1000G_HIGH_COVERAGE ss5623874309 Oct 13, 2022 (156)
59 EVA ss5623985441 Oct 13, 2022 (156)
60 EVA ss5624193805 Oct 13, 2022 (156)
61 SANFORD_IMAGENETICS ss5666149965 Oct 13, 2022 (156)
62 EVA ss5848242897 Oct 13, 2022 (156)
63 1000Genomes NC_000024.9 - 22749853 Oct 12, 2018 (152)
64 1000Genomes_30x NC_000024.10 - 20587967 Oct 13, 2022 (156)
65 chrY_custom_capture NC_000024.9 - 22749853 Apr 27, 2020 (154)
66 Genome-wide autozygosity in Daghestan NC_000024.8 - 21159241 Apr 27, 2020 (154)
67 gnomAD - Genomes NC_000024.10 - 20587967 Apr 27, 2021 (155)
68 Medical Genome Project healthy controls from Spanish population NC_000024.9 - 22749853 Apr 27, 2020 (154)
69 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000024.9 - 22749853 Apr 27, 2021 (155)
70 Qatari NC_000024.9 - 22749853 Apr 27, 2020 (154)
71 SGDP_PRJ NC_000024.9 - 22749853 Apr 27, 2020 (154)
72 ALFA NC_000024.10 - 20587967 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).

Associated ID History Updated (Build)
rs17316213 Oct 07, 2004 (123)
rs34755889 May 23, 2006 (127)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
556035, ss1397805102, ss2635204651, ss3643810234 NC_000024.8:21159240:A:C NC_000024.10:20587966:A:C (self)
84734697, 12682, 709953, 1230337, 21906843, 44791729, ss491581257, ss663101710, ss780681822, ss783355154, ss1399965419, ss1432162008, ss1556781709, ss1711594193, ss1752815127, ss1917716486, ss1939864921, ss1945970323, ss1958181598, ss1958181599, ss2094839181, ss2095230185, ss2711191767, ss2985494935, ss3020974519, ss3023055268, ss3023055269, ss3029951912, ss3630505235, ss3635265380, ss3638887507, ss3640972870, ss3645022138, ss3653613908, ss3653613909, ss3653613910, ss3654261662, ss3744602736, ss3745565378, ss3773056983, ss3788977743, ss3793849517, ss3798734213, ss3836375766, ss3892774749, ss3984446710, ss3984773346, ss3986004410, ss3986888994, ss5237686024, ss5316104173, ss5623985441, ss5624193805, ss5666149965, ss5848242897 NC_000024.9:22749852:A:C NC_000024.10:20587966:A:C (self)
111400244, 595126428, 4708404072, ss2321485323, ss3726714778, ss3823540043, ss4126292037, ss5623874309 NC_000024.10:20587966:A:C NC_000024.10:20587966:A:C (self)
ss23129223, ss24726420, ss50392487, ss75013293, ss172428632 NT_011875.12:8951274:A:C NC_000024.10:20587966:A:C (self)
Help

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

4 citations for rs13447352
PMID Title Author Year Journal
22271044 Y chromosome haplogroups and prostate cancer in populations of European and Ashkenazi Jewish ancestry. Wang Z et al. 2012 Human genetics
31579209 Genotyping of the EIF1AY Gene in Iranian Patients with Non-Obstructive Azoospermia. Yarahmadi E et al. 2019 Current urology
32996047 Risk Y-haplotypes and pathogenic variants of Arab-ancestry boys with autism by an exome-wide association study. Alsubaie LM et al. 2020 Molecular biology reports
35176104 Unveiling forensically relevant biogeographic, phenotype and Y-chromosome SNP variation in Pakistani ethnic groups using a customized hybridisation enrichment forensic intelligence panel. Rauf S et al. 2022 PloS one
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