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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.

rs1491462492

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:116080879-116080881 (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
delTT / dupTT
Variation Type
Indel Insertion and Deletion
Frequency
delTT=0.05048 (1309/25930, 14KJPN)
delTT=0.06717 (1077/16034, 8.3KJPN)
delTT=0.00025 (3/11828, ALFA) (+ 1 more)
delTT=0.055 (33/600, NorthernSweden)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
None
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 11828 TTT=0.99975 T=0.00025, TTTTT=0.00000 0.999493 0.0 0.000507 0
European Sub 7596 TTT=0.9997 T=0.0003, TTTTT=0.0000 0.999473 0.0 0.000527 0
African Sub 2814 TTT=0.9996 T=0.0004, TTTTT=0.0000 0.999289 0.0 0.000711 0
African Others Sub 108 TTT=1.000 T=0.000, TTTTT=0.000 1.0 0.0 0.0 N/A
African American Sub 2706 TTT=0.9996 T=0.0004, TTTTT=0.0000 0.999261 0.0 0.000739 0
Asian Sub 106 TTT=1.000 T=0.000, TTTTT=0.000 1.0 0.0 0.0 N/A
East Asian Sub 84 TTT=1.00 T=0.00, TTTTT=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 22 TTT=1.00 T=0.00, TTTTT=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 146 TTT=1.000 T=0.000, TTTTT=0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 610 TTT=1.000 T=0.000, TTTTT=0.000 1.0 0.0 0.0 N/A
South Asian Sub 86 TTT=1.00 T=0.00, TTTTT=0.00 1.0 0.0 0.0 N/A
Other Sub 470 TTT=1.000 T=0.000, TTTTT=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
14KJPN JAPANESE Study-wide 25930 TTT=0.94952 delTT=0.05048
8.3KJPN JAPANESE Study-wide 16034 TTT=0.93283 delTT=0.06717
Allele Frequency Aggregator Total Global 11828 TTT=0.99975 delTT=0.00025, dupTT=0.00000
Allele Frequency Aggregator European Sub 7596 TTT=0.9997 delTT=0.0003, dupTT=0.0000
Allele Frequency Aggregator African Sub 2814 TTT=0.9996 delTT=0.0004, dupTT=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 TTT=1.000 delTT=0.000, dupTT=0.000
Allele Frequency Aggregator Other Sub 470 TTT=1.000 delTT=0.000, dupTT=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 TTT=1.000 delTT=0.000, dupTT=0.000
Allele Frequency Aggregator Asian Sub 106 TTT=1.000 delTT=0.000, dupTT=0.000
Allele Frequency Aggregator South Asian Sub 86 TTT=1.00 delTT=0.00, dupTT=0.00
Northern Sweden ACPOP Study-wide 600 TTT=0.945 delTT=0.055
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 1 NC_000001.11:g.116080880_116080881del
GRCh38.p14 chr 1 NC_000001.11:g.116080880_116080881dup
GRCh37.p13 chr 1 NC_000001.10:g.116623501_116623502del
GRCh37.p13 chr 1 NC_000001.10:g.116623501_116623502dup
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 TTT= delTT dupTT
GRCh38.p14 chr 1 NC_000001.11:g.116080879_116080881= NC_000001.11:g.116080880_116080881del NC_000001.11:g.116080880_116080881dup
GRCh37.p13 chr 1 NC_000001.10:g.116623500_116623502= NC_000001.10:g.116623501_116623502del NC_000001.10:g.116623501_116623502dup
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#.

8 SubSNP, 6 Frequency submissions
No Submitter Submission ID Date (Build)
1 ACPOP ss3727417710 Jul 12, 2019 (153)
2 EVA ss3826387483 Apr 25, 2020 (154)
3 GNOMAD ss4001017504 Apr 25, 2021 (155)
4 GNOMAD ss4001017505 Apr 25, 2021 (155)
5 TOMMO_GENOMICS ss5145828981 Apr 25, 2021 (155)
6 1000G_HIGH_COVERAGE ss5243722821 Oct 12, 2022 (156)
7 HUGCELL_USP ss5444635927 Oct 12, 2022 (156)
8 TOMMO_GENOMICS ss5671141690 Oct 12, 2022 (156)
9 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 23656521 (NC_000001.11:116080878::TT 13/87534)
Row 23656522 (NC_000001.11:116080878:TT: 5672/87196)

- Apr 25, 2021 (155)
10 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 23656521 (NC_000001.11:116080878::TT 13/87534)
Row 23656522 (NC_000001.11:116080878:TT: 5672/87196)

- Apr 25, 2021 (155)
11 Northern Sweden NC_000001.10 - 116623500 Jul 12, 2019 (153)
12 8.3KJPN NC_000001.10 - 116623500 Apr 25, 2021 (155)
13 14KJPN NC_000001.11 - 116080879 Oct 12, 2022 (156)
14 ALFA NC_000001.11 - 116080879 Apr 25, 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
702575, 3798288, ss3727417710, ss3826387483, ss5145828981 NC_000001.10:116623499:TT: NC_000001.11:116080878:TTT:T (self)
4978794, ss4001017505, ss5243722821, ss5444635927, ss5671141690 NC_000001.11:116080878:TT: NC_000001.11:116080878:TTT:T (self)
13930145587 NC_000001.11:116080878:TTT:T NC_000001.11:116080878:TTT:T (self)
ss4001017504 NC_000001.11:116080878::TT NC_000001.11:116080878:TTT:TTTTT (self)
13930145587 NC_000001.11:116080878:TTT:TTTTT NC_000001.11:116080878:TTT:TTTTT (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 rs1491462492

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