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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.

rs9786465

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chrY:10152006 (GRCh38.p13) 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
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.23638 (3028/12810, ALFA)
G=0.0003 (1/2930, KOREAN)
G=0.000 (0/306, SGDP_PRJ) (+ 3 more)
G=0.05 (3/56, Siberian)
G=0.12 (6/48, Ancient Sardinia)
G=0.02 (1/48, Vietnamese)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
None
Publications
0 citations
Genomic View
See rs on genome
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.p13 chr Y NC_000024.10:g.10152006G>A
GRCh37.p13 chr Y NC_000024.9:g.9989615G>A
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

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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 12810 G=0.23638 A=0.76362
European Sub 10598 G=0.24939 A=0.75061
African Sub 314 G=0.099 A=0.901
African Others Sub 16 G=0.00 A=1.00
African American Sub 298 G=0.104 A=0.896
Asian Sub 166 G=0.000 A=1.000
East Asian Sub 120 G=0.000 A=1.000
Other Asian Sub 46 G=0.00 A=1.00
Latin American 1 Sub 82 G=0.21 A=0.79
Latin American 2 Sub 780 G=0.228 A=0.772
South Asian Sub 6 G=0.0 A=1.0
Other Sub 864 G=0.184 A=0.816


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
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.0003 A=0.9997
SGDP_PRJ Global Study-wide 306 G=0.000 A=1.000
Siberian Global Study-wide 56 G=0.05 A=0.95
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 48 G=0.12 A=0.88
A Vietnamese Genetic Variation Database Global Study-wide 48 G=0.02 A=0.98
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
GRCh38.p13 chr Y NC_000024.10:g.10152006= NC_000024.10:g.10152006G>A
GRCh37.p13 chr Y NC_000024.9:g.9989615= NC_000024.9:g.9989615G>A
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#.

58 SubSNP, 6 Frequency submissions
No Submitter Submission ID Date (Build)
1 WI_SSAHASNP ss13606766 Dec 05, 2003 (119)
2 PERLEGEN ss24723670 Sep 20, 2004 (124)
3 ENSEMBL ss144437454 Dec 01, 2009 (131)
4 GMI ss157821224 Dec 01, 2009 (131)
5 ILLUMINA ss161011489 Dec 01, 2009 (131)
6 COMPLETE_GENOMICS ss162980051 Jul 04, 2010 (132)
7 ILLUMINA ss174895758 Jul 04, 2010 (132)
8 BUSHMAN ss204408433 Jul 04, 2010 (132)
9 BCM-HGSC-SUB ss208946548 Jul 04, 2010 (132)
10 GMI ss283913785 May 04, 2012 (137)
11 GMI ss287661317 Apr 25, 2013 (138)
12 ILLUMINA ss481975111 May 04, 2012 (137)
13 ILLUMINA ss482008812 May 04, 2012 (137)
14 ILLUMINA ss482962537 Sep 08, 2015 (146)
15 ILLUMINA ss485781050 May 04, 2012 (137)
16 ILLUMINA ss537626694 Jul 19, 2016 (147)
17 TISHKOFF ss567113256 Apr 25, 2013 (138)
18 ILLUMINA ss779052725 Sep 08, 2015 (146)
19 ILLUMINA ss783336392 Sep 08, 2015 (146)
20 ILLUMINA ss784287924 Sep 08, 2015 (146)
21 ILLUMINA ss832598207 Sep 08, 2015 (146)
22 ILLUMINA ss834515710 Sep 08, 2015 (146)
23 DDI ss1432152240 Apr 01, 2015 (144)
24 ILLUMINA ss1752816083 Sep 08, 2015 (146)
25 ILLUMINA ss1958171706 Feb 12, 2016 (147)
26 ILLUMINA ss1958171707 Feb 12, 2016 (147)
27 ILLUMINA ss1958171708 Feb 12, 2016 (147)
28 ILLUMINA ss2094838310 Dec 20, 2016 (150)
29 USC_VALOUEV ss2159318757 Dec 20, 2016 (150)
30 SYSTEMSBIOZJU ss2629803530 Nov 08, 2017 (151)
31 ILLUMINA ss2634993280 Nov 08, 2017 (151)
32 GRF ss2710426946 Nov 08, 2017 (151)
33 SWEGEN ss3020872256 Nov 08, 2017 (151)
34 ILLUMINA ss3023050907 Nov 08, 2017 (151)
35 ILLUMINA ss3023050908 Nov 08, 2017 (151)
36 ILLUMINA ss3632876680 Oct 12, 2018 (152)
37 ILLUMINA ss3633570469 Oct 12, 2018 (152)
38 ILLUMINA ss3634300790 Oct 12, 2018 (152)
39 ILLUMINA ss3635264560 Oct 12, 2018 (152)
40 ILLUMINA ss3635977640 Oct 12, 2018 (152)
41 ILLUMINA ss3637014649 Oct 12, 2018 (152)
42 ILLUMINA ss3637731349 Oct 12, 2018 (152)
43 ILLUMINA ss3638886461 Oct 12, 2018 (152)
44 ILLUMINA ss3640972049 Oct 12, 2018 (152)
45 ILLUMINA ss3641564578 Oct 12, 2018 (152)
46 ILLUMINA ss3653609371 Oct 12, 2018 (152)
47 ILLUMINA ss3653609372 Oct 12, 2018 (152)
48 ILLUMINA ss3745564585 Jul 14, 2019 (153)
49 ILLUMINA ss3773056192 Jul 14, 2019 (153)
50 PACBIO ss3788974763 Jul 14, 2019 (153)
51 PACBIO ss3793844260 Jul 14, 2019 (153)
52 PACBIO ss3798729160 Jul 14, 2019 (153)
53 KHV_HUMAN_GENOMES ss3823533817 Jul 14, 2019 (153)
54 EVA ss3836372166 Apr 27, 2020 (154)
55 SGDP_PRJ ss3892641652 Apr 27, 2020 (154)
56 KRGDB ss3943357048 Apr 27, 2020 (154)
57 EVA ss3984771565 Apr 27, 2021 (155)
58 EVA ss3985983695 Apr 27, 2021 (155)
59 KOREAN population from KRGDB NC_000024.9 - 9989615 Apr 27, 2020 (154)
60 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000024.9 - 9989615 Apr 27, 2021 (155)
61 SGDP_PRJ NC_000024.9 - 9989615 Apr 27, 2020 (154)
62 Siberian NC_000024.9 - 9989615 Apr 27, 2020 (154)
63 A Vietnamese Genetic Variation Database NC_000024.9 - 9989615 Jul 14, 2019 (153)
64 ALFA NC_000024.10 - 10152006 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)
rs17306600 Dec 02, 2004 (124)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss162980051, ss204408433, ss208946548, ss283913785, ss287661317, ss481975111 NC_000024.8:10599614:G:A NC_000024.10:10152005:G:A (self)
50534442, 1209622, 44658632, 11835111, 10242890, ss482008812, ss482962537, ss485781050, ss537626694, ss567113256, ss779052725, ss783336392, ss784287924, ss832598207, ss834515710, ss1432152240, ss1752816083, ss1958171706, ss1958171707, ss1958171708, ss2094838310, ss2159318757, ss2629803530, ss2634993280, ss2710426946, ss3020872256, ss3023050907, ss3023050908, ss3632876680, ss3633570469, ss3634300790, ss3635264560, ss3635977640, ss3637014649, ss3637731349, ss3638886461, ss3640972049, ss3641564578, ss3653609371, ss3653609372, ss3745564585, ss3773056192, ss3788974763, ss3793844260, ss3798729160, ss3836372166, ss3892641652, ss3943357048, ss3984771565, ss3985983695 NC_000024.9:9989614:G:A NC_000024.10:10152005:G:A (self)
2313773716, ss3823533817 NC_000024.10:10152005:G:A NC_000024.10:10152005:G:A (self)
ss13606766, ss24723670, ss144437454, ss157821224, ss161011489, ss174895758 NT_011878.9:698292:G:A NC_000024.10:10152005:G: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 rs9786465

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.post596+ae089ad