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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.

rs1459950082

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr18:55631326 (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
G>C / G>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.000004 (1/264690, TOPMED)
C=0.000007 (1/140258, GnomAD)
T=0.00000 (0/10680, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
TCF4 : Synonymous 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 10680 G=1.00000 T=0.00000 1.0 0.0 0.0 N/A
European Sub 6962 G=1.0000 T=0.0000 1.0 0.0 0.0 N/A
African Sub 2294 G=1.0000 T=0.0000 1.0 0.0 0.0 N/A
African Others Sub 84 G=1.00 T=0.00 1.0 0.0 0.0 N/A
African American Sub 2210 G=1.0000 T=0.0000 1.0 0.0 0.0 N/A
Asian Sub 108 G=1.000 T=0.000 1.0 0.0 0.0 N/A
East Asian Sub 84 G=1.00 T=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 24 G=1.00 T=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 146 G=1.000 T=0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 610 G=1.000 T=0.000 1.0 0.0 0.0 N/A
South Asian Sub 94 G=1.00 T=0.00 1.0 0.0 0.0 N/A
Other Sub 466 G=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
TopMed Global Study-wide 264690 G=0.999996 T=0.000004
gnomAD - Genomes Global Study-wide 140258 G=0.999993 C=0.000007
gnomAD - Genomes European Sub 75956 G=1.00000 C=0.00000
gnomAD - Genomes African Sub 42034 G=1.00000 C=0.00000
gnomAD - Genomes American Sub 13660 G=0.99993 C=0.00007
gnomAD - Genomes Ashkenazi Jewish Sub 3322 G=1.0000 C=0.0000
gnomAD - Genomes East Asian Sub 3132 G=1.0000 C=0.0000
gnomAD - Genomes Other Sub 2154 G=1.0000 C=0.0000
Allele Frequency Aggregator Total Global 10680 G=1.00000 T=0.00000
Allele Frequency Aggregator European Sub 6962 G=1.0000 T=0.0000
Allele Frequency Aggregator African Sub 2294 G=1.0000 T=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 G=1.000 T=0.000
Allele Frequency Aggregator Other Sub 466 G=1.000 T=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 G=1.000 T=0.000
Allele Frequency Aggregator Asian Sub 108 G=1.000 T=0.000
Allele Frequency Aggregator South Asian Sub 94 G=1.00 T=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 18 NC_000018.10:g.55631326G>C
GRCh38.p14 chr 18 NC_000018.10:g.55631326G>T
GRCh37.p13 chr 18 NC_000018.9:g.53298557G>C
GRCh37.p13 chr 18 NC_000018.9:g.53298557G>T
TCF4 RefSeqGene NG_011716.2:g.9668C>G
TCF4 RefSeqGene NG_011716.2:g.9668C>A
Gene: TCF4, transcription factor 4 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
TCF4 transcript variant 1 NM_001083962.2:c. N/A Genic Upstream Transcript Variant
TCF4 transcript variant 4 NM_001243227.2:c. N/A Genic Upstream Transcript Variant
TCF4 transcript variant 5 NM_001243228.2:c. N/A Genic Upstream Transcript Variant
TCF4 transcript variant 6 NM_001243230.2:c. N/A Genic Upstream Transcript Variant
TCF4 transcript variant 7 NM_001243231.2:c. N/A Genic Upstream Transcript Variant
TCF4 transcript variant 8 NM_001243232.1:c. N/A Genic Upstream Transcript Variant
TCF4 transcript variant 9 NM_001243233.2:c. N/A Genic Upstream Transcript Variant
TCF4 transcript variant 10 NM_001243234.2:c. N/A Genic Upstream Transcript Variant
TCF4 transcript variant 11 NM_001243235.2:c. N/A Genic Upstream Transcript Variant
TCF4 transcript variant 12 NM_001243236.2:c. N/A Genic Upstream Transcript Variant
TCF4 transcript variant 13 NM_001306207.1:c. N/A Genic Upstream Transcript Variant
TCF4 transcript variant 14 NM_001306208.1:c. N/A Genic Upstream Transcript Variant
TCF4 transcript variant 15 NM_001330604.3:c. N/A Genic Upstream Transcript Variant
TCF4 transcript variant 16 NM_001330605.3:c. N/A Genic Upstream Transcript Variant
TCF4 transcript variant 17 NM_001348211.2:c. N/A Genic Upstream Transcript Variant
TCF4 transcript variant 18 NM_001348212.2:c. N/A Genic Upstream Transcript Variant
TCF4 transcript variant 19 NM_001348213.2:c. N/A Genic Upstream Transcript Variant
TCF4 transcript variant 20 NM_001348214.2:c. N/A Genic Upstream Transcript Variant
TCF4 transcript variant 21 NM_001348215.2:c. N/A Genic Upstream Transcript Variant
TCF4 transcript variant 22 NM_001348216.2:c. N/A Genic Upstream Transcript Variant
TCF4 transcript variant 23 NM_001348217.1:c. N/A Genic Upstream Transcript Variant
TCF4 transcript variant 24 NM_001348218.2:c. N/A Genic Upstream Transcript Variant
TCF4 transcript variant 25 NM_001348219.2:c. N/A Genic Upstream Transcript Variant
TCF4 transcript variant 26 NM_001348220.1:c. N/A Genic Upstream Transcript Variant
TCF4 transcript variant 27 NM_001369567.1:c. N/A Genic Upstream Transcript Variant
TCF4 transcript variant 28 NM_001369568.1:c. N/A Genic Upstream Transcript Variant
TCF4 transcript variant 29 NM_001369569.1:c. N/A Genic Upstream Transcript Variant
TCF4 transcript variant 30 NM_001369570.1:c. N/A Genic Upstream Transcript Variant
TCF4 transcript variant 31 NM_001369571.1:c. N/A Genic Upstream Transcript Variant
TCF4 transcript variant 32 NM_001369572.1:c. N/A Genic Upstream Transcript Variant
TCF4 transcript variant 33 NM_001369573.1:c. N/A Genic Upstream Transcript Variant
TCF4 transcript variant 34 NM_001369574.1:c. N/A Genic Upstream Transcript Variant
TCF4 transcript variant 35 NM_001369575.1:c. N/A Genic Upstream Transcript Variant
TCF4 transcript variant 36 NM_001369576.1:c. N/A Genic Upstream Transcript Variant
TCF4 transcript variant 37 NM_001369577.1:c. N/A Genic Upstream Transcript Variant
TCF4 transcript variant 38 NM_001369578.1:c. N/A Genic Upstream Transcript Variant
TCF4 transcript variant 39 NM_001369579.1:c. N/A Genic Upstream Transcript Variant
TCF4 transcript variant 40 NM_001369580.1:c. N/A Genic Upstream Transcript Variant
TCF4 transcript variant 41 NM_001369581.1:c. N/A Genic Upstream Transcript Variant
TCF4 transcript variant 42 NM_001369582.1:c. N/A Genic Upstream Transcript Variant
TCF4 transcript variant 43 NM_001369583.1:c. N/A Genic Upstream Transcript Variant
TCF4 transcript variant 44 NM_001369584.1:c. N/A Genic Upstream Transcript Variant
TCF4 transcript variant 45 NM_001369585.1:c. N/A Genic Upstream Transcript Variant
TCF4 transcript variant 46 NM_001369586.1:c. N/A Genic Upstream Transcript Variant
TCF4 transcript variant 2 NM_003199.3:c. N/A Genic Upstream Transcript Variant
TCF4 transcript variant 3 NM_001243226.3:c.258C>G T [ACC] > T [ACG] Coding Sequence Variant
transcription factor 4 isoform c precursor NP_001230155.2:p.Thr86= T (Thr) > T (Thr) Synonymous Variant
TCF4 transcript variant 3 NM_001243226.3:c.258C>A T [ACC] > T [ACA] Coding Sequence Variant
transcription factor 4 isoform c precursor NP_001230155.2:p.Thr86= T (Thr) > T (Thr) Synonymous 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 G= C T
GRCh38.p14 chr 18 NC_000018.10:g.55631326= NC_000018.10:g.55631326G>C NC_000018.10:g.55631326G>T
GRCh37.p13 chr 18 NC_000018.9:g.53298557= NC_000018.9:g.53298557G>C NC_000018.9:g.53298557G>T
TCF4 RefSeqGene NG_011716.2:g.9668= NG_011716.2:g.9668C>G NG_011716.2:g.9668C>A
TCF4 transcript variant 3 NM_001243226.3:c.258= NM_001243226.3:c.258C>G NM_001243226.3:c.258C>A
TCF4 transcript variant 3 NM_001243226.2:c.258= NM_001243226.2:c.258C>G NM_001243226.2:c.258C>A
TCF4 transcript variant 3 NM_001243226.1:c.258= NM_001243226.1:c.258C>G NM_001243226.1:c.258C>A
transcription factor 4 isoform c precursor NP_001230155.2:p.Thr86= NP_001230155.2:p.Thr86= NP_001230155.2:p.Thr86=
transcription factor 4 isoform c NP_001230155.1:p.Thr86= NP_001230155.1:p.Thr86= NP_001230155.1:p.Thr86=
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#.

4 SubSNP, 3 Frequency submissions
No Submitter Submission ID Date (Build)
1 GNOMAD ss2743310215 Nov 08, 2017 (151)
2 GNOMAD ss2749962600 Nov 08, 2017 (151)
3 GNOMAD ss2957332629 Nov 08, 2017 (151)
4 TOPMED ss5058735654 Apr 27, 2021 (155)
5 gnomAD - Genomes NC_000018.10 - 55631326 Apr 27, 2021 (155)
6 TopMed NC_000018.10 - 55631326 Apr 27, 2021 (155)
7 ALFA NC_000018.10 - 55631326 Apr 27, 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
ss2743310215, ss2749962600, ss2957332629 NC_000018.9:53298556:G:C NC_000018.10:55631325:G:C (self)
526198085 NC_000018.10:55631325:G:C NC_000018.10:55631325:G:C (self)
274281317, 1757924477, ss5058735654 NC_000018.10:55631325:G:T NC_000018.10:55631325:G:T (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 rs1459950082

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