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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.

rs1491357807

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr11:5657599-5657600 (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
delAA
Variation Type
Deletion
Frequency
delAA=0.00369 (326/88398, GnomAD)
delAA=0.00021 (6/28024, 14KJPN)
delAA=0.00012 (2/16556, 8.3KJPN) (+ 1 more)
delAA=0.00000 (0/11684, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
TRIM5 : Intron Variant
LOC107984302 : 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 11684 AA=1.00000 =0.00000 1.0 0.0 0.0 N/A
European Sub 7612 AA=1.0000 =0.0000 1.0 0.0 0.0 N/A
African Sub 2660 AA=1.0000 =0.0000 1.0 0.0 0.0 N/A
African Others Sub 96 AA=1.00 =0.00 1.0 0.0 0.0 N/A
African American Sub 2564 AA=1.0000 =0.0000 1.0 0.0 0.0 N/A
Asian Sub 108 AA=1.000 =0.000 1.0 0.0 0.0 N/A
East Asian Sub 84 AA=1.00 =0.00 1.0 0.0 0.0 N/A
Other Asian Sub 24 AA=1.00 =0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 142 AA=1.000 =0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 606 AA=1.000 =0.000 1.0 0.0 0.0 N/A
South Asian Sub 94 AA=1.00 =0.00 1.0 0.0 0.0 N/A
Other Sub 462 AA=1.000 =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
gnomAD - Genomes Global Study-wide 88398 AA=0.99631 delAA=0.00369
gnomAD - Genomes European Sub 55984 AA=0.99959 delAA=0.00041
gnomAD - Genomes African Sub 21366 AA=0.98652 delAA=0.01348
gnomAD - Genomes American Sub 6144 AA=0.9980 delAA=0.0020
gnomAD - Genomes Ashkenazi Jewish Sub 2614 AA=1.0000 delAA=0.0000
gnomAD - Genomes Other Sub 1308 AA=0.9992 delAA=0.0008
gnomAD - Genomes East Asian Sub 982 AA=0.998 delAA=0.002
14KJPN JAPANESE Study-wide 28024 AA=0.99979 delAA=0.00021
8.3KJPN JAPANESE Study-wide 16556 AA=0.99988 delAA=0.00012
Allele Frequency Aggregator Total Global 11684 AA=1.00000 delAA=0.00000
Allele Frequency Aggregator European Sub 7612 AA=1.0000 delAA=0.0000
Allele Frequency Aggregator African Sub 2660 AA=1.0000 delAA=0.0000
Allele Frequency Aggregator Latin American 2 Sub 606 AA=1.000 delAA=0.000
Allele Frequency Aggregator Other Sub 462 AA=1.000 delAA=0.000
Allele Frequency Aggregator Latin American 1 Sub 142 AA=1.000 delAA=0.000
Allele Frequency Aggregator Asian Sub 108 AA=1.000 delAA=0.000
Allele Frequency Aggregator South Asian Sub 94 AA=1.00 delAA=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.5657599_5657600del
GRCh37.p13 chr 11 NC_000011.9:g.5678829_5678830del
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 X8 XM_047427783.1:c.794+8056…

XM_047427783.1:c.794+8056_794+8057del

 		N/A Intron Variant
TRIM5 transcript variant X12 XM_047427784.1:c.745-1173…

XM_047427784.1:c.745-11737_745-11736del

 		N/A Intron 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 X6 XR_001748014.3:n. N/A Intron Variant
TRIM5 transcript variant X7 XR_007062517.1: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 X13 XR_007062520.1:n. N/A Intron Variant
TRIM5 transcript variant X14 XR_007062521.1:n. N/A Intron Variant
TRIM5 transcript variant X15 XR_007062522.1:n. N/A Intron Variant
Gene: LOC107984302, uncharacterized LOC107984302 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
LOC107984302 transcript XR_001748100.1:n. 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 AA= delAA
GRCh38.p14 chr 11 NC_000011.10:g.5657599_5657600= NC_000011.10:g.5657599_5657600del
GRCh37.p13 chr 11 NC_000011.9:g.5678829_5678830= NC_000011.9:g.5678829_5678830del
TRIM5 transcript variant X4 XM_005253186.1:c.745-1910= XM_005253186.1:c.745-1911_745-1910del
TRIM5 transcript variant X8 XM_047427783.1:c.794+8057= XM_047427783.1:c.794+8056_794+8057del
TRIM5 transcript variant X12 XM_047427784.1:c.745-11736= XM_047427784.1:c.745-11737_745-11736del
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#.

6 SubSNP, 4 Frequency submissions
No Submitter Submission ID Date (Build)
1 GNOMAD ss4229361086 Apr 26, 2021 (155)
2 TOMMO_GENOMICS ss5200506321 Apr 26, 2021 (155)
3 1000G_HIGH_COVERAGE ss5286264597 Oct 16, 2022 (156)
4 HUGCELL_USP ss5481582138 Oct 16, 2022 (156)
5 SANFORD_IMAGENETICS ss5650556228 Oct 16, 2022 (156)
6 TOMMO_GENOMICS ss5747210406 Oct 16, 2022 (156)
7 gnomAD - Genomes NC_000011.10 - 5657599 Apr 26, 2021 (155)
8 8.3KJPN NC_000011.9 - 5678829 Apr 26, 2021 (155)
9 14KJPN NC_000011.10 - 5657599 Oct 16, 2022 (156)
10 ALFA NC_000011.10 - 5657599 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
58475628, ss5200506321, ss5650556228 NC_000011.9:5678828:AA: NC_000011.10:5657598:AA: (self)
370215440, 81047510, 12795361530, ss4229361086, ss5286264597, ss5481582138, ss5747210406 NC_000011.10:5657598:AA: NC_000011.10:5657598:AA: (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 rs1491357807

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