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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.


Current Build 155

Released April 9, 2021

Homo sapiens
chrY:19466414 (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.

Variation Type
SNV Single Nucleotide Variation
A=0.00051 (15/29449, GnomAD)
A=0.0312 (115/3688, ALFA)
A=0.00 (0/26, Ancient Sardinia)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
BCORP1 : Intron Variant
0 citations
Genomic View
See rs on genome

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.19466414G>A
GRCh37.p13 chr Y NC_000024.9:g.21628300G>A
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

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 3688 G=0.9688 A=0.0312
European Sub 3560 G=0.9683 A=0.0317
African Sub 38 G=1.00 A=0.00
African Others Sub 0 G=0 A=0
African American Sub 38 G=1.00 A=0.00
Asian Sub 8 G=1.0 A=0.0
East Asian Sub 8 G=1.0 A=0.0
Other Asian Sub 0 G=0 A=0
Latin American 1 Sub 4 G=1.0 A=0.0
Latin American 2 Sub 28 G=1.00 A=0.00
South Asian Sub 4 G=1.0 A=0.0
Other Sub 46 G=0.96 A=0.04


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").

Study Population Group Sample Size Ref Allele Alt Allele
gnomAD - Genomes Global Study-wide 29449 G=0.99949 A=0.00051
gnomAD - Genomes European Sub 16040 G=0.99956 A=0.00044
gnomAD - Genomes African Sub 8300 G=0.9999 A=0.0001
gnomAD - Genomes American Sub 3173 G=0.9981 A=0.0019
gnomAD - Genomes East Asian Sub 746 G=1.000 A=0.000
gnomAD - Genomes Ashkenazi Jewish Sub 737 G=1.000 A=0.000
gnomAD - Genomes Other Sub 453 G=0.998 A=0.002
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 26 G=1.00 A=0.00

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.19466414= NC_000024.10:g.19466414G>A
GRCh37.p13 chr Y NC_000024.9:g.21628300= NC_000024.9:g.21628300G>A

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#.

11 SubSNP, 3 Frequency submissions
No Submitter Submission ID Date (Build)
1 PAGE ss50392490 Mar 14, 2006 (126)
2 ILLUMINA ss834162684 Aug 21, 2014 (142)
3 HUMAN_LONGEVITY ss2321472345 Dec 20, 2016 (150)
4 ILLUMINA ss2634994607 Nov 08, 2017 (151)
5 ILLUMINA ss2711191700 Nov 08, 2017 (151)
6 ILLUMINA ss3632877494 Oct 12, 2018 (152)
7 ILLUMINA ss3641266532 Oct 12, 2018 (152)
8 ILLUMINA ss3641565508 Oct 12, 2018 (152)
9 EVA ss3984773068 Apr 27, 2021 (155)
10 EVA ss3986001589 Apr 27, 2021 (155)
11 GNOMAD ss4126252846 Apr 27, 2021 (155)
12 gnomAD - Genomes NC_000024.10 - 19466414 Apr 27, 2021 (155)
13 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000024.9 - 21628300 Apr 27, 2021 (155)
14 ALFA NC_000024.10 - 19466414 Apr 27, 2021 (155)

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
1227516, ss834162684, ss2634994607, ss2711191700, ss3632877494, ss3641266532, ss3641565508, ss3984773068, ss3986001589 NC_000024.9:21628299:G:A NC_000024.10:19466413:G:A (self)
595086877, 6021307728, ss2321472345, ss4126252846 NC_000024.10:19466413:G:A NC_000024.10:19466413:G:A (self)
ss50392490 NT_011875.12:7829721:G:A NC_000024.10:19466413:G:A (self)

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

No publications for rs35169834


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