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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.

rs9341289

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chrY:12908393 (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
T>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.00052 (16/30733, GnomAD)
G=0.007 (6/896, chrY)
T=0.0 (0/8, SGDP_PRJ) (+ 1 more)
G=0.0 (0/4, Ancient Sardinia)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
DDX3Y : Intron Variant
Publications
0 citations
Genomic View
See rs on genome
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 30733 T=0.99948 G=0.00052
gnomAD - Genomes European Sub 16613 T=0.99982 G=0.00018
gnomAD - Genomes African Sub 8645 T=0.9986 G=0.0014
gnomAD - Genomes American Sub 3432 T=0.9997 G=0.0003
gnomAD - Genomes East Asian Sub 798 T=1.000 G=0.000
gnomAD - Genomes Ashkenazi Jewish Sub 757 T=1.000 G=0.000
gnomAD - Genomes Other Sub 488 T=1.000 G=0.000
chrY_custom_capture Global Study-wide 896 T=0.993 G=0.007
chrY_custom_capture AFP Sub 0 T=0 G=0
chrY_custom_capture AHG Sub 0 T=0 G=0
chrY_custom_capture ASC Sub 0 T=0 G=0
chrY_custom_capture ASE Sub 0 T=0 G=0
chrY_custom_capture AUS Sub 0 T=0 G=0
chrY_custom_capture BRI Sub 0 T=0 G=0
chrY_custom_capture ENV Sub 0 T=0 G=0
chrY_custom_capture ESC Sub 0 T=0 G=0
chrY_custom_capture ESE Sub 0 T=0 G=0
chrY_custom_capture ESW Sub 0 T=0 G=0
chrY_custom_capture MEX Sub 0 T=0 G=0
chrY_custom_capture MNE Sub 0 T=0 G=0
chrY_custom_capture SCA Sub 0 T=0 G=0
SGDP_PRJ Global Study-wide 8 T=0.0 G=1.0
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 4 T=1.0 G=0.0
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.12908393T>G
GRCh37.p13 chr Y NC_000024.9:g.15020304T>G
DDX3Y RefSeqGene NG_012831.1:g.9286T>G
Gene: DDX3Y, DEAD-box helicase 3 Y-linked (plus strand)
Molecule type Change Amino acid[Codon] SO Term
DDX3Y transcript variant 1 NM_001122665.3:c.103+799T…

NM_001122665.3:c.103+799T>G

 		N/A Intron Variant
DDX3Y transcript variant 3 NM_001302552.3:c.94+799T>G N/A Intron Variant
DDX3Y transcript variant 4 NM_001324195.2:c.103+799T…

NM_001324195.2:c.103+799T>G

 		N/A Intron Variant
DDX3Y transcript variant 2 NM_004660.5:c.103+799T>G N/A Intron Variant
DDX3Y transcript variant 5 NR_136716.2:n. N/A Intron Variant
DDX3Y transcript variant 6 NR_136717.2:n. N/A Intron Variant
DDX3Y transcript variant 7 NR_136718.2:n. N/A Intron Variant
DDX3Y transcript variant 8 NR_136719.2:n. N/A Intron Variant
DDX3Y transcript variant 9 NR_136720.2:n. N/A Intron Variant
DDX3Y transcript variant 10 NR_136721.2:n. N/A Intron Variant
DDX3Y transcript variant 11 NR_136722.1:n. N/A Intron Variant
DDX3Y transcript variant 12 NR_136723.1:n. N/A Intron Variant
DDX3Y transcript variant 13 NR_136724.1:n. N/A Intron Variant
DDX3Y transcript variant X1 XM_047442775.1:c.103+799T…

XM_047442775.1:c.103+799T>G

 		N/A Intron Variant
DDX3Y transcript variant X2 XM_047442776.1:c.94+799T>G N/A Intron Variant
DDX3Y transcript variant X3 XM_047442777.1:c.103+799T…

XM_047442777.1:c.103+799T>G

 		N/A Intron Variant
DDX3Y transcript variant X4 XM_047442778.1:c.-320+799…

XM_047442778.1:c.-320+799T>G

 		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 T= G
GRCh38.p14 chr Y NC_000024.10:g.12908393= NC_000024.10:g.12908393T>G
GRCh37.p13 chr Y NC_000024.9:g.15020304= NC_000024.9:g.15020304T>G
DDX3Y RefSeqGene NG_012831.1:g.9286= NG_012831.1:g.9286T>G
DDX3Y transcript variant 1 NM_001122665.1:c.103+799= NM_001122665.1:c.103+799T>G
DDX3Y transcript variant 1 NM_001122665.3:c.103+799= NM_001122665.3:c.103+799T>G
DDX3Y transcript variant 3 NM_001302552.3:c.94+799= NM_001302552.3:c.94+799T>G
DDX3Y transcript variant 4 NM_001324195.2:c.103+799= NM_001324195.2:c.103+799T>G
DDX3Y transcript variant 2 NM_004660.3:c.103+799= NM_004660.3:c.103+799T>G
DDX3Y transcript variant 2 NM_004660.5:c.103+799= NM_004660.5:c.103+799T>G
DDX3Y transcript variant X1 XM_005262564.1:c.94+799= XM_005262564.1:c.94+799T>G
DDX3Y transcript variant X1 XM_047442775.1:c.103+799= XM_047442775.1:c.103+799T>G
DDX3Y transcript variant X2 XM_047442776.1:c.94+799= XM_047442776.1:c.94+799T>G
DDX3Y transcript variant X3 XM_047442777.1:c.103+799= XM_047442777.1:c.103+799T>G
DDX3Y transcript variant X4 XM_047442778.1:c.-320+799= XM_047442778.1:c.-320+799T>G
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#.

9 SubSNP, 4 Frequency submissions
No Submitter Submission ID Date (Build)
1 OEFNER ss12724441 Dec 05, 2003 (119)
2 HUMGEN ss778077567 Aug 21, 2014 (142)
3 CDBUSTAMANTE ss825683146 Aug 21, 2014 (142)
4 JOBLING_UOL ss1399956633 Apr 01, 2015 (144)
5 HUMAN_LONGEVITY ss2321407543 Dec 20, 2016 (150)
6 HUMGEN ss3029947745 Nov 08, 2017 (151)
7 SGDP_PRJ ss3892704342 Apr 27, 2020 (154)
8 EVA ss3985988339 Apr 27, 2021 (155)
9 GNOMAD ss4126128127 Apr 27, 2021 (155)
10 chrY_custom_capture NC_000024.9 - 15020304 Apr 27, 2020 (154)
11 gnomAD - Genomes NC_000024.10 - 12908393 Apr 27, 2021 (155)
12 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000024.9 - 15020304 Apr 27, 2021 (155)
13 SGDP_PRJ NC_000024.9 - 15020304 Apr 27, 2020 (154)
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
3908, 1214266, 44721322, ss778077567, ss825683146, ss1399956633, ss3029947745, ss3892704342, ss3985988339 NC_000024.9:15020303:T:G NC_000024.10:12908392:T:G (self)
594961993, ss2321407543, ss4126128127 NC_000024.10:12908392:T:G NC_000024.10:12908392:T:G (self)
ss12724441 NT_011875.12:1221725:T:G NC_000024.10:12908392:T:G (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 rs9341289

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