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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.

rs66965464

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chrY:19484824 (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=0.16473 (4804/29162, GnomAD)
T=0.2320 (371/1599, 1000G_30x)
T=0.2125 (262/1233, 1000G) (+ 5 more)
T=0.054 (48/896, chrY)
T=0.276 (58/210, ALFA)
T=0.08 (4/53, Qatari)
T=0.00 (0/42, Ancient Sardinia)
C=0.00 (0/26, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
BCORP1 : Intron Variant
LOC102723934 : 2KB Upstream 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: 20231103111315
Population Group Sample Size Ref Allele Alt Allele Ref HMOZ Alt HMOZ HTRZ HWEP
Total Global 210 C=0.724 T=0.276 0.72381 0.27619 0.0 32
European Sub 36 C=1.00 T=0.00 1.0 0.0 0.0 N/A
African Sub 104 C=0.481 T=0.519 0.480769 0.519231 0.0 28
African Others Sub 0 C=0 T=0 0 0 0 N/A
African American Sub 104 C=0.481 T=0.519 0.480769 0.519231 0.0 28
Asian Sub 26 C=1.00 T=0.00 1.0 0.0 0.0 N/A
East Asian Sub 26 C=1.00 T=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 0 C=0 T=0 0 0 0 N/A
Latin American 1 Sub 0 C=0 T=0 0 0 0 N/A
Latin American 2 Sub 0 C=0 T=0 0 0 0 N/A
South Asian Sub 6 C=1.0 T=0.0 1.0 0.0 0.0 N/A
Other Sub 38 C=0.89 T=0.11 0.894737 0.105263 0.0 11


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
gnomAD - Genomes Global Study-wide 29162 C=0.83527 T=0.16473
gnomAD - Genomes European Sub 16096 C=0.99814 T=0.00186
gnomAD - Genomes African Sub 7832 C=0.4115 T=0.5885
gnomAD - Genomes American Sub 3287 C=0.9653 T=0.0347
gnomAD - Genomes Ashkenazi Jewish Sub 750 C=1.000 T=0.000
gnomAD - Genomes East Asian Sub 743 C=1.000 T=0.000
gnomAD - Genomes Other Sub 454 C=0.888 T=0.112
1000Genomes_30x Global Study-wide 1599 C=0.7680 T=0.2320
1000Genomes_30x African Sub 458 C=0.214 T=0.786
1000Genomes_30x South Asian Sub 319 C=1.000 T=0.000
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=0.951 T=0.049
1000Genomes Global Study-wide 1233 C=0.7875 T=0.2125
1000Genomes African Sub 319 C=0.204 T=0.796
1000Genomes South Asian Sub 260 C=1.000 T=0.000
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=0.953 T=0.047
chrY_custom_capture Global Study-wide 896 C=0.946 T=0.054
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
Allele Frequency Aggregator Total Global 210 C=0.724 T=0.276
Allele Frequency Aggregator African Sub 104 C=0.481 T=0.519
Allele Frequency Aggregator Other Sub 38 C=0.89 T=0.11
Allele Frequency Aggregator European Sub 36 C=1.00 T=0.00
Allele Frequency Aggregator Asian Sub 26 C=1.00 T=0.00
Allele Frequency Aggregator South Asian Sub 6 C=1.0 T=0.0
Allele Frequency Aggregator Latin American 1 Sub 0 C=0 T=0
Allele Frequency Aggregator Latin American 2 Sub 0 C=0 T=0
Qatari Global Study-wide 53 C=0.92 T=0.08
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 42 C=1.00 T=0.00
SGDP_PRJ Global Study-wide 26 C=0.00 T=1.00
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.19484824C>T
GRCh37.p13 chr Y NC_000024.9:g.21646710C>T
Gene: BCORP1, BCL6 corepressor pseudogene 1 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
BCORP1 transcript variant 2 NR_002923.2:n. N/A Intron Variant
BCORP1 transcript variant 1 NR_033732.1:n. N/A Intron Variant
Gene: LOC102723934, uncharacterized LOC102723934 (minus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
LOC102723934 transcript XM_047442786.1:c. N/A Upstream Transcript 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.19484824= NC_000024.10:g.19484824C>T
GRCh37.p13 chr Y NC_000024.9:g.21646710= NC_000024.9:g.21646710C>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#.

21 SubSNP, 8 Frequency submissions
No Submitter Submission ID Date (Build)
1 PAGE ss106476162 Feb 04, 2009 (130)
2 ILLUMINA-UK ss115582274 Feb 04, 2009 (130)
3 BUSHMAN ss204419244 Jul 04, 2010 (132)
4 TISHKOFF ss567116267 Apr 25, 2013 (138)
5 CDBUSTAMANTE ss825688152 Aug 21, 2014 (142)
6 JOBLING_UOL ss1399964600 Apr 01, 2015 (144)
7 1000GENOMES ss1556777346 Apr 01, 2015 (144)
8 WEILL_CORNELL_DGM ss1939864356 Feb 12, 2016 (147)
9 ILLUMINA ss1958180418 Feb 12, 2016 (147)
10 HUMAN_LONGEVITY ss2321472551 Dec 20, 2016 (150)
11 ILLUMINA ss3023054833 Nov 08, 2017 (151)
12 HUMGEN ss3029951530 Nov 08, 2017 (151)
13 ILLUMINA ss3653613444 Oct 12, 2018 (152)
14 ILLUMINA ss3726714452 Jul 14, 2019 (153)
15 KHV_HUMAN_GENOMES ss3823539286 Jul 14, 2019 (153)
16 SGDP_PRJ ss3892750733 Apr 27, 2020 (154)
17 EVA ss3984773074 Apr 27, 2021 (155)
18 EVA ss3986001652 Apr 27, 2021 (155)
19 GNOMAD ss4126253230 Apr 27, 2021 (155)
20 1000G_HIGH_COVERAGE ss5623860034 Oct 13, 2022 (156)
21 SANFORD_IMAGENETICS ss5666144472 Oct 13, 2022 (156)
22 1000Genomes NC_000024.9 - 21646710 Oct 12, 2018 (152)
23 1000Genomes_30x NC_000024.10 - 19484824 Oct 13, 2022 (156)
24 chrY_custom_capture NC_000024.9 - 21646710 Apr 27, 2020 (154)
25 gnomAD - Genomes NC_000024.10 - 19484824 Apr 27, 2021 (155)
26 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000024.9 - 21646710 Apr 27, 2021 (155)
27 Qatari NC_000024.9 - 21646710 Apr 27, 2020 (154)
28 SGDP_PRJ NC_000024.9 - 21646710 Apr 27, 2020 (154)
29 ALFA NC_000024.10 - 19484824 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)
rs66965465 Feb 26, 2009 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss204419244 NC_000024.8:20106097:C:T NC_000024.10:19484823:C:T (self)
84730334, 11863, 1227579, 21906278, 44767713, ss567116267, ss825688152, ss1399964600, ss1556777346, ss1939864356, ss1958180418, ss3023054833, ss3029951530, ss3653613444, ss3892750733, ss3984773074, ss3986001652, ss5666144472 NC_000024.9:21646709:C:T NC_000024.10:19484823:C:T (self)
111385969, 595087261, 10468681784, ss2321472551, ss3726714452, ss3823539286, ss4126253230, ss5623860034 NC_000024.10:19484823:C:T NC_000024.10:19484823:C:T (self)
ss106476162, ss115582274 NT_011875.12:7848131:C:T NC_000024.10:19484823: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 rs66965464

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.post820+afb47a3d