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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.

rs1491192958

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr2:66639598-66639601 (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
delTA
Variation Type
Indel Insertion and Deletion
Frequency
delTA=0.00647 (602/93090, GnomAD)
delTA=0.00392 (64/16314, ALFA)
delTA=0.0025 (16/6404, 1000G_30x) (+ 1 more)
delTA=0.003 (2/600, NorthernSweden)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LINC01798 : 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 16314 TATA=0.99608 TA=0.00392 0.992154 0.0 0.007846 0
European Sub 12062 TATA=0.99519 TA=0.00481 0.990383 0.0 0.009617 0
African Sub 2816 TATA=0.9986 TA=0.0014 0.997159 0.0 0.002841 0
African Others Sub 108 TATA=1.000 TA=0.000 1.0 0.0 0.0 N/A
African American Sub 2708 TATA=0.9985 TA=0.0015 0.997046 0.0 0.002954 0
Asian Sub 108 TATA=1.000 TA=0.000 1.0 0.0 0.0 N/A
East Asian Sub 84 TATA=1.00 TA=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 24 TATA=1.00 TA=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 146 TATA=0.993 TA=0.007 0.986301 0.0 0.013699 0
Latin American 2 Sub 610 TATA=0.998 TA=0.002 0.996721 0.0 0.003279 0
South Asian Sub 94 TATA=1.00 TA=0.00 1.0 0.0 0.0 N/A
Other Sub 478 TATA=1.000 TA=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 93090 TATA=0.99353 delTA=0.00647
gnomAD - Genomes European Sub 56432 TATA=0.99086 delTA=0.00914
gnomAD - Genomes African Sub 22078 TATA=0.99751 delTA=0.00249
gnomAD - Genomes American Sub 8852 TATA=0.9971 delTA=0.0029
gnomAD - Genomes Ashkenazi Jewish Sub 2610 TATA=1.0000 delTA=0.0000
gnomAD - Genomes East Asian Sub 1656 TATA=1.0000 delTA=0.0000
gnomAD - Genomes Other Sub 1462 TATA=0.9966 delTA=0.0034
Allele Frequency Aggregator Total Global 16314 TATA=0.99608 delTA=0.00392
Allele Frequency Aggregator European Sub 12062 TATA=0.99519 delTA=0.00481
Allele Frequency Aggregator African Sub 2816 TATA=0.9986 delTA=0.0014
Allele Frequency Aggregator Latin American 2 Sub 610 TATA=0.998 delTA=0.002
Allele Frequency Aggregator Other Sub 478 TATA=1.000 delTA=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 TATA=0.993 delTA=0.007
Allele Frequency Aggregator Asian Sub 108 TATA=1.000 delTA=0.000
Allele Frequency Aggregator South Asian Sub 94 TATA=1.00 delTA=0.00
1000Genomes_30x Global Study-wide 6404 TATA=0.9975 delTA=0.0025
1000Genomes_30x African Sub 1786 TATA=1.0000 delTA=0.0000
1000Genomes_30x Europe Sub 1266 TATA=0.9913 delTA=0.0087
1000Genomes_30x South Asian Sub 1202 TATA=0.9975 delTA=0.0025
1000Genomes_30x East Asian Sub 1170 TATA=1.0000 delTA=0.0000
1000Genomes_30x American Sub 980 TATA=0.998 delTA=0.002
Northern Sweden ACPOP Study-wide 600 TATA=0.997 delTA=0.003
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 2 NC_000002.12:g.66639598TA[1]
GRCh37.p13 chr 2 NC_000002.11:g.66866730TA[1]
Gene: LINC01798, long intergenic non-protein coding RNA 1798 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LINC01798 transcript NR_110156.1: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 TATA= delTA
GRCh38.p14 chr 2 NC_000002.12:g.66639598_66639601= NC_000002.12:g.66639598TA[1]
GRCh37.p13 chr 2 NC_000002.11:g.66866730_66866733= NC_000002.11:g.66866730TA[1]
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, 4 Frequency submissions
No Submitter Submission ID Date (Build)
1 GNOMAD ss2774659962 Jan 10, 2018 (151)
2 SWEGEN ss2989667581 Jan 10, 2018 (151)
3 EVA_DECODE ss3704089330 Jul 13, 2019 (153)
4 ACPOP ss3728518694 Jul 13, 2019 (153)
5 1000G_HIGH_COVERAGE ss5248410605 Oct 12, 2022 (156)
6 HUGCELL_USP ss5448581518 Oct 12, 2022 (156)
7 1000G_HIGH_COVERAGE ss5523819156 Oct 12, 2022 (156)
8 SANFORD_IMAGENETICS ss5628936906 Oct 12, 2022 (156)
9 1000Genomes_30x NC_000002.12 - 66639598 Oct 12, 2022 (156)
10 gnomAD - Genomes NC_000002.12 - 66639598 Apr 26, 2021 (155)
11 Northern Sweden NC_000002.11 - 66866730 Jul 13, 2019 (153)
12 ALFA NC_000002.12 - 66639598 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
1803559, ss2774659962, ss2989667581, ss3728518694, ss5628936906 NC_000002.11:66866729:TA: NC_000002.12:66639597:TATA:TA (self)
11345091, 61149930, ss3704089330, ss5248410605, ss5448581518, ss5523819156 NC_000002.12:66639597:TA: NC_000002.12:66639597:TATA:TA (self)
6347676118 NC_000002.12:66639597:TATA:TA NC_000002.12:66639597:TATA:TA (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 rs1491192958

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