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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.

rs1491575021

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr11:5623126-5623128 (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
delAT
Variation Type
Indel Insertion and Deletion
Frequency
delAT=0.00000 (0/11862, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
TRIM34 : Intron Variant
TRIM5 : Intron Variant
TRIM6-TRIM34 : 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 11862 TAT=1.00000 T=0.00000 1.0 0.0 0.0 N/A
European Sub 7618 TAT=1.0000 T=0.0000 1.0 0.0 0.0 N/A
African Sub 2816 TAT=1.0000 T=0.0000 1.0 0.0 0.0 N/A
African Others Sub 108 TAT=1.000 T=0.000 1.0 0.0 0.0 N/A
African American Sub 2708 TAT=1.0000 T=0.0000 1.0 0.0 0.0 N/A
Asian Sub 108 TAT=1.000 T=0.000 1.0 0.0 0.0 N/A
East Asian Sub 84 TAT=1.00 T=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 24 TAT=1.00 T=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 146 TAT=1.000 T=0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 610 TAT=1.000 T=0.000 1.0 0.0 0.0 N/A
South Asian Sub 94 TAT=1.00 T=0.00 1.0 0.0 0.0 N/A
Other Sub 470 TAT=1.000 T=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
Allele Frequency Aggregator Total Global 11862 TAT=1.00000 delAT=0.00000
Allele Frequency Aggregator European Sub 7618 TAT=1.0000 delAT=0.0000
Allele Frequency Aggregator African Sub 2816 TAT=1.0000 delAT=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 TAT=1.000 delAT=0.000
Allele Frequency Aggregator Other Sub 470 TAT=1.000 delAT=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 TAT=1.000 delAT=0.000
Allele Frequency Aggregator Asian Sub 108 TAT=1.000 delAT=0.000
Allele Frequency Aggregator South Asian Sub 94 TAT=1.00 delAT=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 11 NC_000011.10:g.5623127_5623128del
GRCh37.p13 chr 11 NC_000011.9:g.5644357_5644358del
Gene: TRIM6-TRIM34, TRIM6-TRIM34 readthrough (plus strand)
Molecule type Change Amino acid[Codon] SO Term
TRIM6-TRIM34 transcript NM_001003819.4:c.986-9128…

NM_001003819.4:c.986-9128_986-9127del

 		N/A Intron Variant
Gene: TRIM34, tripartite motif containing 34 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
TRIM34 transcript variant 4 NM_001003827.1:c.-78+3104…

NM_001003827.1:c.-78+3104_-78+3105del

 		N/A Intron Variant
TRIM34 transcript variant 1 NM_021616.6:c. N/A Genic Upstream Transcript Variant
TRIM34 transcript variant 3 NM_130390.2:c. N/A Genic Upstream Transcript Variant
Gene: TRIM5, tripartite motif containing 5 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
TRIM5 transcript variant alpha NM_033034.3:c. N/A Genic Downstream Transcript Variant
TRIM5 transcript variant gamma NM_033092.4:c. N/A Genic Downstream Transcript Variant
TRIM5 transcript variant delta NM_033093.4:c. N/A Genic Downstream Transcript Variant
TRIM5 transcript variant X1 XM_005253183.4:c. N/A Genic Downstream Transcript Variant
TRIM5 transcript variant X2 XM_005253184.4:c. N/A Genic Downstream Transcript Variant
TRIM5 transcript variant X11 XM_006718358.4:c. N/A Genic Downstream Transcript Variant
TRIM5 transcript variant X4 XM_011520426.4:c. N/A Genic Downstream Transcript Variant
TRIM5 transcript variant X3 XM_017018460.3:c. N/A Genic Downstream Transcript Variant
TRIM5 transcript variant X5 XM_017018461.3:c. N/A Genic Downstream Transcript Variant
TRIM5 transcript variant X12 XM_017018463.3:c. N/A Genic Downstream Transcript Variant
TRIM5 transcript variant X8 XM_047427783.1:c. N/A Genic Downstream Transcript Variant
TRIM5 transcript variant X12 XM_047427784.1:c. N/A Genic Downstream Transcript Variant
TRIM5 transcript variant X6 XR_001748014.3:n. N/A Intron Variant
TRIM5 transcript variant X9 XR_007062518.1:n. N/A Intron Variant
TRIM5 transcript variant X10 XR_007062519.1:n. N/A Intron Variant
TRIM5 transcript variant X15 XR_007062522.1:n. N/A Intron Variant
TRIM5 transcript variant X7 XR_007062517.1:n. N/A Genic Downstream Transcript Variant
TRIM5 transcript variant X13 XR_007062520.1:n. N/A Genic Downstream Transcript Variant
TRIM5 transcript variant X14 XR_007062521.1:n. N/A Genic Downstream 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 TAT= delAT
GRCh38.p14 chr 11 NC_000011.10:g.5623126_5623128= NC_000011.10:g.5623127_5623128del
GRCh37.p13 chr 11 NC_000011.9:g.5644356_5644358= NC_000011.9:g.5644357_5644358del
TRIM6-TRIM34 transcript NM_001003819.3:c.986-9129= NM_001003819.3:c.986-9128_986-9127del
TRIM6-TRIM34 transcript NM_001003819.4:c.986-9129= NM_001003819.4:c.986-9128_986-9127del
TRIM34 transcript variant 4 NM_001003827.1:c.-78+3103= NM_001003827.1:c.-78+3104_-78+3105del
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 Frequency submission
No Submitter Submission ID Date (Build)
1 ALFA NC_000011.10 - 5623126 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
10461141278 NC_000011.10:5623125:TAT:T NC_000011.10:5623125:TAT:T (self)
Removed from this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Destination RSIDs
ss3136045019 NC_000011.10:5623125:TA: NC_000011.10:5623125:TAT:T
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 rs1491575021

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