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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.

rs2032607

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chrY:12792926 (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
C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.00208 (170/81572, ALFA)
T=0.00189 (57/30237, GnomAD)
T=0.0194 (31/1599, 1000G_30x) (+ 7 more)
T=0.0219 (27/1233, 1000G)
T=0.011 (10/896, chrY)
T=0.034 (28/816, Daghestan)
T=0.000 (0/102, HapMap)
T=0.04 (2/53, Qatari)
T=0.00 (0/20, Ancient Sardinia)
C=0.0 (0/10, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
USP9Y : 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 81572 C=0.99792 T=0.00208
European Sub 73856 C=0.99828 T=0.00172
African Sub 1554 C=0.9987 T=0.0013
African Others Sub 66 C=1.00 T=0.00
African American Sub 1488 C=0.9987 T=0.0013
Asian Sub 2026 C=0.9990 T=0.0010
East Asian Sub 1632 C=0.9988 T=0.0012
Other Asian Sub 394 C=1.000 T=0.000
Latin American 1 Sub 316 C=0.994 T=0.006
Latin American 2 Sub 1590 C=0.9987 T=0.0013
South Asian Sub 144 C=0.861 T=0.139
Other Sub 2086 C=0.9928 T=0.0072


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 81572 C=0.99792 T=0.00208
Allele Frequency Aggregator European Sub 73856 C=0.99828 T=0.00172
Allele Frequency Aggregator Other Sub 2086 C=0.9928 T=0.0072
Allele Frequency Aggregator Asian Sub 2026 C=0.9990 T=0.0010
Allele Frequency Aggregator Latin American 2 Sub 1590 C=0.9987 T=0.0013
Allele Frequency Aggregator African Sub 1554 C=0.9987 T=0.0013
Allele Frequency Aggregator Latin American 1 Sub 316 C=0.994 T=0.006
Allele Frequency Aggregator South Asian Sub 144 C=0.861 T=0.139
gnomAD - Genomes Global Study-wide 30237 C=0.99811 T=0.00189
gnomAD - Genomes European Sub 16372 C=0.99866 T=0.00134
gnomAD - Genomes African Sub 8528 C=0.9993 T=0.0007
gnomAD - Genomes American Sub 3339 C=0.9928 T=0.0072
gnomAD - Genomes East Asian Sub 791 C=0.999 T=0.001
gnomAD - Genomes Ashkenazi Jewish Sub 748 C=0.996 T=0.004
gnomAD - Genomes Other Sub 459 C=0.998 T=0.002
1000Genomes_30x Global Study-wide 1599 C=0.9806 T=0.0194
1000Genomes_30x African Sub 458 C=1.000 T=0.000
1000Genomes_30x South Asian Sub 319 C=0.903 T=0.097
1000Genomes_30x Europe Sub 305 C=1.000 T=0.000
1000Genomes_30x East Asian Sub 292 C=1.000 T=0.000
1000Genomes_30x American Sub 225 C=1.000 T=0.000
1000Genomes Global Study-wide 1233 C=0.9781 T=0.0219
1000Genomes African Sub 319 C=1.000 T=0.000
1000Genomes South Asian Sub 260 C=0.896 T=0.104
1000Genomes East Asian Sub 244 C=1.000 T=0.000
1000Genomes Europe Sub 240 C=1.000 T=0.000
1000Genomes American Sub 170 C=1.000 T=0.000
chrY_custom_capture Global Study-wide 896 C=0.989 T=0.011
chrY_custom_capture AFP Sub 0 C=0 T=0
chrY_custom_capture AHG Sub 0 C=0 T=0
chrY_custom_capture ASC Sub 0 C=0 T=0
chrY_custom_capture ASE Sub 0 C=0 T=0
chrY_custom_capture AUS Sub 0 C=0 T=0
chrY_custom_capture BRI Sub 0 C=0 T=0
chrY_custom_capture ENV Sub 0 C=0 T=0
chrY_custom_capture ESC Sub 0 C=0 T=0
chrY_custom_capture ESE Sub 0 C=0 T=0
chrY_custom_capture ESW Sub 0 C=0 T=0
chrY_custom_capture MEX Sub 0 C=0 T=0
chrY_custom_capture MNE Sub 0 C=0 T=0
chrY_custom_capture SCA Sub 0 C=0 T=0
Genome-wide autozygosity in Daghestan Global Study-wide 816 C=0.966 T=0.034
Genome-wide autozygosity in Daghestan Daghestan Sub 308 C=0.981 T=0.019
Genome-wide autozygosity in Daghestan Near_East Sub 144 C=0.944 T=0.056
Genome-wide autozygosity in Daghestan Central Asia Sub 122 C=0.967 T=0.033
Genome-wide autozygosity in Daghestan Europe Sub 108 C=1.000 T=0.000
Genome-wide autozygosity in Daghestan South Asian Sub 98 C=0.90 T=0.10
Genome-wide autozygosity in Daghestan Caucasus Sub 36 C=1.00 T=0.00
HapMap Global Study-wide 102 C=1.000 T=0.000
HapMap African Sub 60 C=1.00 T=0.00
HapMap Asian Sub 42 C=1.00 T=0.00
Qatari Global Study-wide 53 C=0.96 T=0.04
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 20 C=1.00 T=0.00
SGDP_PRJ Global Study-wide 10 C=0.0 T=1.0
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.12792926C>T
GRCh37.p13 chr Y NC_000024.9:g.14904859C>T
USP9Y RefSeqGene NG_008311.2:g.96697C>T
USP9Y RefSeqGene NG_008311.1:g.96700C>T
Gene: USP9Y, ubiquitin specific peptidase 9 Y-linked (plus strand)
Molecule type Change Amino acid[Codon] SO Term
USP9Y transcript NM_004654.4:c.3814-106C>T N/A Intron Variant
USP9Y transcript variant X1 XM_047442771.1:c.3580-106…

XM_047442771.1:c.3580-106C>T

 		N/A Intron Variant
USP9Y transcript variant X2 XM_047442772.1:c.3814-106…

XM_047442772.1:c.3814-106C>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 C= T
GRCh38.p14 chr Y NC_000024.10:g.12792926= NC_000024.10:g.12792926C>T
GRCh37.p13 chr Y NC_000024.9:g.14904859= NC_000024.9:g.14904859C>T
USP9Y RefSeqGene NG_008311.2:g.96697= NG_008311.2:g.96697C>T
USP9Y RefSeqGene NG_008311.1:g.96700= NG_008311.1:g.96700C>T
USP9Y transcript NM_004654.3:c.3814-106= NM_004654.3:c.3814-106C>T
USP9Y transcript NM_004654.4:c.3814-106= NM_004654.4:c.3814-106C>T
USP9Y transcript variant X1 XM_047442771.1:c.3580-106= XM_047442771.1:c.3580-106C>T
USP9Y transcript variant X2 XM_047442772.1:c.3814-106= XM_047442772.1:c.3814-106C>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#.

56 SubSNP, 10 Frequency submissions
No Submitter Submission ID Date (Build)
1 OEFNER ss2941571 Apr 12, 2001 (94)
2 ILLUMINA ss74963235 Dec 07, 2007 (129)
3 ILLUMINA ss160491197 Dec 01, 2009 (131)
4 ILLUMINA ss173056777 Jul 04, 2010 (132)
5 ILLUMINA ss480389174 May 04, 2012 (137)
6 ILLUMINA ss480402079 May 04, 2012 (137)
7 ILLUMINA ss481180111 Sep 08, 2015 (146)
8 ILLUMINA ss484992213 May 04, 2012 (137)
9 ILLUMINA ss537025884 Jul 19, 2016 (147)
10 ILLUMINA ss779037565 Sep 08, 2015 (146)
11 ILLUMINA ss782942405 Sep 08, 2015 (146)
12 ILLUMINA ss783904958 Sep 08, 2015 (146)
13 CDBUSTAMANTE ss825683048 Aug 21, 2014 (142)
14 ILLUMINA ss832198088 Sep 08, 2015 (146)
15 ILLUMINA ss834500358 Sep 08, 2015 (146)
16 HAMMER_LAB ss1397804251 Sep 08, 2015 (146)
17 JOBLING_UOL ss1399956492 Apr 01, 2015 (144)
18 DDI ss1432160186 Apr 01, 2015 (144)
19 1000GENOMES ss1556749508 Apr 01, 2015 (144)
20 ILLUMINA ss1752814329 Sep 08, 2015 (146)
21 WEILL_CORNELL_DGM ss1939860603 Feb 12, 2016 (147)
22 ILLUMINA ss1945968739 Feb 12, 2016 (147)
23 ILLUMINA ss1958176255 Feb 12, 2016 (147)
24 ILLUMINA ss2094838424 Dec 20, 2016 (150)
25 ILLUMINA ss2095229503 Dec 20, 2016 (150)
26 HUMAN_LONGEVITY ss2321406344 Dec 20, 2016 (150)
27 ILLUMINA ss2634993939 Nov 08, 2017 (151)
28 ILLUMINA ss3023053120 Nov 08, 2017 (151)
29 ILLUMINA ss3626005359 Oct 12, 2018 (152)
30 ILLUMINA ss3630504290 Oct 12, 2018 (152)
31 ILLUMINA ss3632876841 Oct 12, 2018 (152)
32 ILLUMINA ss3633570580 Oct 12, 2018 (152)
33 ILLUMINA ss3634300913 Oct 12, 2018 (152)
34 ILLUMINA ss3635264695 Oct 12, 2018 (152)
35 ILLUMINA ss3635977745 Oct 12, 2018 (152)
36 ILLUMINA ss3637014813 Oct 12, 2018 (152)
37 ILLUMINA ss3637731467 Oct 12, 2018 (152)
38 ILLUMINA ss3638886638 Oct 12, 2018 (152)
39 ILLUMINA ss3640972183 Oct 12, 2018 (152)
40 ILLUMINA ss3641265901 Oct 12, 2018 (152)
41 ILLUMINA ss3641564823 Oct 12, 2018 (152)
42 ILLUMINA ss3643809417 Oct 12, 2018 (152)
43 ILLUMINA ss3645021321 Oct 12, 2018 (152)
44 ILLUMINA ss3653611603 Oct 12, 2018 (152)
45 ILLUMINA ss3726713238 Jul 14, 2019 (153)
46 ILLUMINA ss3744336175 Jul 14, 2019 (153)
47 ILLUMINA ss3745564710 Jul 14, 2019 (153)
48 ILLUMINA ss3773056318 Jul 14, 2019 (153)
49 SGDP_PRJ ss3892703726 Apr 27, 2020 (154)
50 EVA ss3985988032 Apr 27, 2021 (155)
51 GNOMAD ss4126125797 Apr 27, 2021 (155)
52 EVA ss5237629862 Apr 27, 2021 (155)
53 1000G_HIGH_COVERAGE ss5623817856 Oct 17, 2022 (156)
54 SANFORD_IMAGENETICS ss5666136551 Oct 17, 2022 (156)
55 EVA ss5848242371 Oct 17, 2022 (156)
56 EVA ss5979925283 Oct 17, 2022 (156)
57 1000Genomes NC_000024.9 - 14904859 Oct 12, 2018 (152)
58 1000Genomes_30x NC_000024.10 - 12792926 Oct 17, 2022 (156)
59 chrY_custom_capture NC_000024.9 - 14904859 Apr 27, 2020 (154)
60 Genome-wide autozygosity in Daghestan NC_000024.8 - 13414253 Apr 27, 2020 (154)
61 gnomAD - Genomes NC_000024.10 - 12792926 Apr 27, 2021 (155)
62 HapMap NC_000024.10 - 12792926 Apr 27, 2020 (154)
63 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000024.9 - 14904859 Apr 27, 2021 (155)
64 Qatari NC_000024.9 - 14904859 Apr 27, 2020 (154)
65 SGDP_PRJ NC_000024.9 - 14904859 Apr 27, 2020 (154)
66 ALFA NC_000024.10 - 12792926 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
555449, ss480389174, ss1397804251, ss3643809417 NC_000024.8:13414252:C:T NC_000024.10:12792925:C:T (self)
84702496, 3767, 1213959, 21902525, 44720706, ss480402079, ss481180111, ss484992213, ss537025884, ss779037565, ss782942405, ss783904958, ss825683048, ss832198088, ss834500358, ss1399956492, ss1432160186, ss1556749508, ss1752814329, ss1939860603, ss1945968739, ss1958176255, ss2094838424, ss2095229503, ss2634993939, ss3023053120, ss3626005359, ss3630504290, ss3632876841, ss3633570580, ss3634300913, ss3635264695, ss3635977745, ss3637014813, ss3637731467, ss3638886638, ss3640972183, ss3641265901, ss3641564823, ss3645021321, ss3653611603, ss3744336175, ss3745564710, ss3773056318, ss3892703726, ss3985988032, ss5237629862, ss5666136551, ss5848242371, ss5979925283 NC_000024.9:14904858:C:T NC_000024.10:12792925:C:T (self)
111343791, 594959662, 4060633, 9888814245, ss2321406344, ss3726713238, ss4126125797, ss5623817856 NC_000024.10:12792925:C:T NC_000024.10:12792925:C:T (self)
ss2941571, ss74963235, ss160491197, ss173056777 NT_011875.12:1106280:C:T NC_000024.10:12792925:C: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 rs2032607

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