Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

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.

rs10465459

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chrY:18992437 (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
G>A / G>C / G>T
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.23025 (2373/10306, ALFA)
G=0.1224 (758/6193, ExAC)
G=0.2372 (695/2930, KOREAN) (+ 4 more)
G=0.313 (174/556, SGDP_PRJ)
G=0.225 (120/534, MGP)
G=0.29 (16/56, Siberian)
G=0.0 (0/3, Vietnamese)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
TTTY14 : 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 10306 G=0.23025 A=0.76975
European Sub 7168 G=0.2268 A=0.7732
African Sub 670 G=0.224 A=0.776
African Others Sub 12 G=0.17 A=0.83
African American Sub 658 G=0.225 A=0.775
Asian Sub 64 G=0.20 A=0.80
East Asian Sub 34 G=0.18 A=0.82
Other Asian Sub 30 G=0.23 A=0.77
Latin American 1 Sub 2 G=0.0 A=1.0
Latin American 2 Sub 12 G=0.00 A=1.00
South Asian Sub 0 G=0 A=0
Other Sub 2390 G=0.2444 A=0.7556


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 10306 G=0.23025 A=0.76975
Allele Frequency Aggregator European Sub 7168 G=0.2268 A=0.7732
Allele Frequency Aggregator Other Sub 2390 G=0.2444 A=0.7556
Allele Frequency Aggregator African Sub 670 G=0.224 A=0.776
Allele Frequency Aggregator Asian Sub 64 G=0.20 A=0.80
Allele Frequency Aggregator Latin American 2 Sub 12 G=0.00 A=1.00
Allele Frequency Aggregator Latin American 1 Sub 2 G=0.0 A=1.0
Allele Frequency Aggregator South Asian Sub 0 G=0 A=0
ExAC Global Study-wide 6193 G=0.1224 A=0.8776
ExAC Asian Sub 3247 G=0.0933 A=0.9067
ExAC Europe Sub 2389 G=0.1499 A=0.8501
ExAC African Sub 372 G=0.210 A=0.790
ExAC American Sub 115 G=0.122 A=0.878
ExAC Other Sub 70 G=0.07 A=0.93
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.2372 A=0.7628, C=0.0000, T=0.0000
SGDP_PRJ Global Study-wide 556 G=0.313 A=0.687
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 G=0.225 A=0.775
Siberian Global Study-wide 56 G=0.29 A=0.71
A Vietnamese Genetic Variation Database Global Study-wide 3 G=0.0 A=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.18992437G>A
GRCh38.p14 chr Y NC_000024.10:g.18992437G>C
GRCh38.p14 chr Y NC_000024.10:g.18992437G>T
GRCh37.p13 chr Y NC_000024.9:g.21154323G>A
GRCh37.p13 chr Y NC_000024.9:g.21154323G>C
GRCh37.p13 chr Y NC_000024.9:g.21154323G>T
CD24P4 pseudogene NG_006012.6:g.482C>T
CD24P4 pseudogene NG_006012.6:g.482C>G
CD24P4 pseudogene NG_006012.6:g.482C>A
Gene: TTTY14, testis-specific transcript, Y-linked 14 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
TTTY14 transcript variant 5 NR_001543.4:n. N/A Intron Variant
TTTY14 transcript variant 1 NR_125733.1:n. N/A Intron Variant
TTTY14 transcript variant 2 NR_125734.1:n. N/A Intron Variant
TTTY14 transcript variant 3 NR_125735.1:n. N/A Intron Variant
TTTY14 transcript variant 4 NR_125736.1:n. N/A Intron Variant
TTTY14 transcript variant 6 NR_125737.2:n. N/A Intron Variant
TTTY14 transcript variant 7 NR_158640.1:n. N/A Intron Variant
TTTY14 transcript variant 8 NR_158641.1:n. 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 G= A C T
GRCh38.p14 chr Y NC_000024.10:g.18992437= NC_000024.10:g.18992437G>A NC_000024.10:g.18992437G>C NC_000024.10:g.18992437G>T
GRCh37.p13 chr Y NC_000024.9:g.21154323= NC_000024.9:g.21154323G>A NC_000024.9:g.21154323G>C NC_000024.9:g.21154323G>T
CD24P4 pseudogene NG_006012.6:g.482= NG_006012.6:g.482C>T NG_006012.6:g.482C>G NG_006012.6:g.482C>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#.

54 SubSNP, 7 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss14819479 Dec 05, 2003 (119)
2 CSHL-HAPMAP ss17301793 Feb 27, 2004 (120)
3 SSAHASNP ss22885469 Apr 05, 2004 (121)
4 ABI ss43985772 Mar 13, 2006 (126)
5 HGSV ss78974667 Dec 07, 2007 (129)
6 HGSV ss85528597 Dec 16, 2007 (130)
7 BGI ss105778608 Feb 06, 2009 (130)
8 ENSEMBL ss139786182 Dec 01, 2009 (131)
9 ENSEMBL ss144449626 Dec 01, 2009 (131)
10 GMI ss157863220 Dec 01, 2009 (131)
11 ILLUMINA ss159849426 Dec 01, 2009 (131)
12 COMPLETE_GENOMICS ss166083371 Jul 04, 2010 (132)
13 ILLUMINA ss169061389 Jul 04, 2010 (132)
14 BUSHMAN ss204419067 Jul 04, 2010 (132)
15 BCM-HGSC-SUB ss208946838 Jul 04, 2010 (132)
16 GMI ss283923860 May 04, 2012 (137)
17 GMI ss287666164 Apr 25, 2013 (138)
18 PJP ss294561965 May 09, 2011 (134)
19 ILLUMINA ss479152842 May 04, 2012 (137)
20 ILLUMINA ss479153152 May 04, 2012 (137)
21 ILLUMINA ss479157789 Sep 08, 2015 (146)
22 CLINSEQ_SNP ss491956036 May 04, 2012 (137)
23 TISHKOFF ss567116033 Apr 25, 2013 (138)
24 ILLUMINA ss780636036 Sep 08, 2015 (146)
25 ILLUMINA ss780910171 Sep 08, 2015 (146)
26 ILLUMINA ss783597707 Sep 08, 2015 (146)
27 ILLUMINA ss836130097 Sep 08, 2015 (146)
28 DDI ss1432160904 Apr 01, 2015 (144)
29 EVA_EXAC ss1694670458 Apr 01, 2015 (144)
30 EVA_MGP ss1711594168 Apr 01, 2015 (144)
31 ILLUMINA ss1958180156 Feb 12, 2016 (147)
32 USC_VALOUEV ss2159356846 Dec 20, 2016 (150)
33 SYSTEMSBIOZJU ss2629805521 Nov 08, 2017 (151)
34 ILLUMINA ss2634994543 Nov 08, 2017 (151)
35 GRF ss2710441124 Nov 08, 2017 (151)
36 GNOMAD ss2745637580 Nov 08, 2017 (151)
37 SWEGEN ss3020960304 Nov 08, 2017 (151)
38 ILLUMINA ss3023054662 Nov 08, 2017 (151)
39 ILLUMINA ss3632877431 Oct 12, 2018 (152)
40 ILLUMINA ss3637015401 Oct 12, 2018 (152)
41 ILLUMINA ss3638887289 Oct 12, 2018 (152)
42 ILLUMINA ss3642746553 Oct 12, 2018 (152)
43 OMUKHERJEE_ADBS ss3646579484 Oct 12, 2018 (152)
44 ILLUMINA ss3653613260 Oct 12, 2018 (152)
45 EVA ss3836375074 Apr 27, 2020 (154)
46 SGDP_PRJ ss3892746074 Apr 27, 2020 (154)
47 KRGDB ss3943534156 Apr 27, 2020 (154)
48 FSA-LAB ss3984446691 Apr 27, 2021 (155)
49 EVA ss3986090470 Apr 27, 2021 (155)
50 EVA ss3986888966 Apr 27, 2021 (155)
51 EVA ss5623985434 Oct 13, 2022 (156)
52 EVA ss5624193798 Oct 13, 2022 (156)
53 SANFORD_IMAGENETICS ss5666143619 Oct 13, 2022 (156)
54 EVA ss5981325795 Oct 13, 2022 (156)
55 ExAC NC_000024.9 - 21154323 Oct 12, 2018 (152)
56 KOREAN population from KRGDB NC_000024.9 - 21154323 Apr 27, 2020 (154)
57 Medical Genome Project healthy controls from Spanish population NC_000024.9 - 21154323 Apr 27, 2020 (154)
58 SGDP_PRJ NC_000024.9 - 21154323 Apr 27, 2020 (154)
59 Siberian NC_000024.9 - 21154323 Apr 27, 2020 (154)
60 A Vietnamese Genetic Variation Database NC_000024.9 - 21154323 Jul 14, 2019 (153)
61 ALFA NC_000024.10 - 18992437 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)
rs61616918 May 27, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss78974667, ss85528597 NC_000024.7:19542447:G:A NC_000024.10:18992436:G:A (self)
ss166083371, ss204419067, ss208946838, ss283923860, ss287666164, ss294561965, ss479152842, ss491956036 NC_000024.8:19613710:G:A NC_000024.10:18992436:G:A (self)
10182930, 50711550, 709928, 44763054, 11873200, 10243645, ss479153152, ss479157789, ss567116033, ss780636036, ss780910171, ss783597707, ss836130097, ss1432160904, ss1694670458, ss1711594168, ss1958180156, ss2159356846, ss2629805521, ss2634994543, ss2710441124, ss2745637580, ss3020960304, ss3023054662, ss3632877431, ss3637015401, ss3638887289, ss3642746553, ss3646579484, ss3653613260, ss3836375074, ss3892746074, ss3943534156, ss3984446691, ss3986090470, ss3986888966, ss5623985434, ss5624193798, ss5666143619, ss5981325795 NC_000024.9:21154322:G:A NC_000024.10:18992436:G:A (self)
8190747554 NC_000024.10:18992436:G:A NC_000024.10:18992436:G:A (self)
ss14819479, ss17301793 NT_011875.10:7241657:G:A NC_000024.10:18992436:G:A (self)
ss22885469, ss43985772, ss105778608, ss139786182, ss144449626, ss157863220, ss159849426, ss169061389 NT_011875.12:7355744:G:A NC_000024.10:18992436:G:A (self)
50711550, ss3943534156 NC_000024.9:21154322:G:C NC_000024.10:18992436:G:C (self)
50711550, ss3943534156, ss5981325795 NC_000024.9:21154322:G:T NC_000024.10:18992436:G: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 rs10465459

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