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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.

rs1481943026

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chrX:137032302-137032308 (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
delTTGT
Variation Type
Indel Insertion and Deletion
Frequency
delTTGT=0.000087 (23/264690, TOPMED)
delTTGT=0.000048 (5/103343, GnomAD)
delTTGT=0.00000 (0/14050, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
GPR101 : 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: 20231103111315
Population Group Sample Size Ref Allele Alt Allele Ref HMOZ Alt HMOZ HTRZ HWEP
Total Global 14050 TGTTTGT=1.00000 TGT=0.00000 1.0 0.0 0.0 N/A
European Sub 9690 TGTTTGT=1.0000 TGT=0.0000 1.0 0.0 0.0 N/A
African Sub 2898 TGTTTGT=1.0000 TGT=0.0000 1.0 0.0 0.0 N/A
African Others Sub 114 TGTTTGT=1.000 TGT=0.000 1.0 0.0 0.0 N/A
African American Sub 2784 TGTTTGT=1.0000 TGT=0.0000 1.0 0.0 0.0 N/A
Asian Sub 112 TGTTTGT=1.000 TGT=0.000 1.0 0.0 0.0 N/A
East Asian Sub 86 TGTTTGT=1.00 TGT=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 26 TGTTTGT=1.00 TGT=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 146 TGTTTGT=1.000 TGT=0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 610 TGTTTGT=1.000 TGT=0.000 1.0 0.0 0.0 N/A
South Asian Sub 98 TGTTTGT=1.00 TGT=0.00 1.0 0.0 0.0 N/A
Other Sub 496 TGTTTGT=1.000 TGT=0.000 1.0 0.0 0.0 N/A


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
TopMed Global Study-wide 264690 TGTTTGT=0.999913 delTTGT=0.000087
gnomAD - Genomes Global Study-wide 103343 TGTTTGT=0.999952 delTTGT=0.000048
gnomAD - Genomes European Sub 56838 TGTTTGT=0.99996 delTTGT=0.00004
gnomAD - Genomes African Sub 30921 TGTTTGT=0.99990 delTTGT=0.00010
gnomAD - Genomes American Sub 9294 TGTTTGT=1.0000 delTTGT=0.0000
gnomAD - Genomes Ashkenazi Jewish Sub 2521 TGTTTGT=1.0000 delTTGT=0.0000
gnomAD - Genomes East Asian Sub 2218 TGTTTGT=1.0000 delTTGT=0.0000
gnomAD - Genomes Other Sub 1551 TGTTTGT=1.0000 delTTGT=0.0000
Allele Frequency Aggregator Total Global 14050 TGTTTGT=1.00000 delTTGT=0.00000
Allele Frequency Aggregator European Sub 9690 TGTTTGT=1.0000 delTTGT=0.0000
Allele Frequency Aggregator African Sub 2898 TGTTTGT=1.0000 delTTGT=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 TGTTTGT=1.000 delTTGT=0.000
Allele Frequency Aggregator Other Sub 496 TGTTTGT=1.000 delTTGT=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 TGTTTGT=1.000 delTTGT=0.000
Allele Frequency Aggregator Asian Sub 112 TGTTTGT=1.000 delTTGT=0.000
Allele Frequency Aggregator South Asian Sub 98 TGTTTGT=1.00 delTTGT=0.00
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 X NC_000023.11:g.137032305_137032308del
GRCh37.p13 chr X NC_000023.10:g.136114464_136114467del
GPR101 RefSeqGene (LRG_1000) NG_016367.2:g.6691_6694del
Gene: GPR101, G protein-coupled receptor 101 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
GPR101 transcript NM_054021.2:c.-92-539_-92…

NM_054021.2:c.-92-539_-92-536del

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 TGTTTGT= delTTGT
GRCh38.p14 chr X NC_000023.11:g.137032302_137032308= NC_000023.11:g.137032305_137032308del
GRCh37.p13 chr X NC_000023.10:g.136114461_136114467= NC_000023.10:g.136114464_136114467del
GPR101 RefSeqGene (LRG_1000) NG_016367.2:g.6688_6694= NG_016367.2:g.6691_6694del
GPR101 transcript NM_054021.2:c.-92-536= NM_054021.2:c.-92-539_-92-536del
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#.

2 SubSNP, 3 Frequency submissions
No Submitter Submission ID Date (Build)
1 GNOMAD ss4379247869 Apr 26, 2021 (155)
2 TOPMED ss5138547759 Apr 26, 2021 (155)
3 gnomAD - Genomes NC_000023.11 - 137032302 Apr 26, 2021 (155)
4 TopMed NC_000023.11 - 137032302 Apr 26, 2021 (155)
5 ALFA NC_000023.11 - 137032302 Apr 26, 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
592252795, 702154116, ss4379247869, ss5138547759 NC_000023.11:137032301:TGTT: NC_000023.11:137032301:TGTTTGT:TGT (self)
3611817230 NC_000023.11:137032301:TGTTTGT:TGT NC_000023.11:137032301:TGTTTGT:TGT (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 rs1481943026

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