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dbSNP Short Genetic Variations

Reference SNP (rs) Report

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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.

rs104894977

Current Build 151

Released July 17, 2018

Organism
Homo sapiens
Position
chrY:2787600 (GRCh38.p7) 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
Variation Type
SNV Single Nucleotide Variation
Frequency
None
Clinical Significance
Reported in ClinVar
Gene : Consequence
SRY : Stop Gained
Publications
2 citations
Genomic View
See rs on genome
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.p7 chr Y NC_000024.10:g.2787600G>A
GRCh37.p13 chr Y NC_000024.9:g.2655641G>A
SRY RefSeqGene NG_011751.1:g.5152C>T
Gene: SRY, sex determining region Y (minus strand)
Molecule type Change Amino acid[Codon] SO Term
SRY transcript NM_003140.2:c.4C>T Q [CAA] > * [TAA] Coding Sequence Variant
sex-determining region Y protein NP_003131.1:p.Gln...

NP_003131.1:p.Gln2Ter

Q (Gln) > * (Ter) Stop Gained
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.

Allele: A (allele ID: 24792 )
ClinVar Accession Disease Names Clinical Significance
RCV000010407.4 46,XY sex reversal, type 1 Pathogenic
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").

None
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 Note
GRCh38.p7 chr Y NC_000024.10:g.2787600G= NC_000024.10:g.2787600G>A
GRCh37.p13 chr Y NC_000024.9:g.2655641G= NC_000024.9:g.2655641G>A
SRY RefSeqGene NG_011751.1:g.5152C= NG_011751.1:g.5152C>T
SRY transcript NM_003140.2:c.4C= NM_003140.2:c.4C>T
sex-determining region Y protein NP_003131.1:p.Gln2= NP_003131.1:p.Gln2Ter
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#.

1 ClinVar, 2 SubSNP submissions
No Submitter Submission ID Date (Build)
1 OMICIA ss244240096 Aug 29, 2012 (137)
2 OMIM-CURATED-RECORDS ss342562759 Mar 29, 2011 (133)
3 ClinVar RCV000010407.4 Jul 20, 2018 (151)
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
ss244240096, ss342562759 NC_000024.10:2787599:G= NC_000024.10:2787599:G= (self)
RCV000010407.4, ss244240096, ss342562759 NC_000024.10:2787599:G>A NC_000024.10:2787599:G>A (self)
Help

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

2 citations for rs104894977
PMID Title Author Year Journal
2401216 XY female mice resulting from a heritable mutation in the primary testis-determining gene, Tdy. Lovell-Badge R et al. 1990 Development (Cambridge, England)
9443877 A de novo mutation (Gln2Stop) at the 5' end of the SRY gene leads to sex reversal with partial ovarian function. Brown S et al. 1998 American journal of human genetics

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: 0.1.4.post833+d3ba21e