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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.

rs1484862538

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:117081942 (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
A>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.000004 (1/264690, TOPMED)
T=0.000007 (1/140262, GnomAD)
T=0.00000 (0/14050, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
TTF2 : Missense 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 14050 A=1.00000 T=0.00000 1.0 0.0 0.0 N/A
European Sub 9690 A=1.0000 T=0.0000 1.0 0.0 0.0 N/A
African Sub 2898 A=1.0000 T=0.0000 1.0 0.0 0.0 N/A
African Others Sub 114 A=1.000 T=0.000 1.0 0.0 0.0 N/A
African American Sub 2784 A=1.0000 T=0.0000 1.0 0.0 0.0 N/A
Asian Sub 112 A=1.000 T=0.000 1.0 0.0 0.0 N/A
East Asian Sub 86 A=1.00 T=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 26 A=1.00 T=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 146 A=1.000 T=0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 610 A=1.000 T=0.000 1.0 0.0 0.0 N/A
South Asian Sub 98 A=1.00 T=0.00 1.0 0.0 0.0 N/A
Other Sub 496 A=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 A=0.999996 T=0.000004
gnomAD - Genomes Global Study-wide 140262 A=0.999993 T=0.000007
gnomAD - Genomes European Sub 75938 A=1.00000 T=0.00000
gnomAD - Genomes African Sub 42064 A=0.99998 T=0.00002
gnomAD - Genomes American Sub 13654 A=1.00000 T=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3322 A=1.0000 T=0.0000
gnomAD - Genomes East Asian Sub 3134 A=1.0000 T=0.0000
gnomAD - Genomes Other Sub 2150 A=1.0000 T=0.0000
Allele Frequency Aggregator Total Global 14050 A=1.00000 T=0.00000
Allele Frequency Aggregator European Sub 9690 A=1.0000 T=0.0000
Allele Frequency Aggregator African Sub 2898 A=1.0000 T=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 A=1.000 T=0.000
Allele Frequency Aggregator Other Sub 496 A=1.000 T=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 A=1.000 T=0.000
Allele Frequency Aggregator Asian Sub 112 A=1.000 T=0.000
Allele Frequency Aggregator South Asian Sub 98 A=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 1 NC_000001.11:g.117081942A>T
GRCh37.p13 chr 1 NC_000001.10:g.117624564A>T
Gene: TTF2, transcription termination factor 2 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
TTF2 transcript NM_003594.4:c.1898A>T K [AAA] > I [ATA] Coding Sequence Variant
transcription termination factor 2 NP_003585.3:p.Lys633Ile K (Lys) > I (Ile) Missense Variant
TTF2 transcript variant X1 XM_017002550.3:c.1919A>T K [AAA] > I [ATA] Coding Sequence Variant
transcription termination factor 2 isoform X1 XP_016858039.1:p.Lys640Ile K (Lys) > I (Ile) Missense Variant
TTF2 transcript variant X2 XM_017002551.3:c.1919A>T K [AAA] > I [ATA] Coding Sequence Variant
transcription termination factor 2 isoform X1 XP_016858040.1:p.Lys640Ile K (Lys) > I (Ile) Missense Variant
TTF2 transcript variant X3 XM_017002552.3:c.1916A>T K [AAA] > I [ATA] Coding Sequence Variant
transcription termination factor 2 isoform X2 XP_016858041.1:p.Lys639Ile K (Lys) > I (Ile) Missense Variant
TTF2 transcript variant X4 XM_047432135.1:c.1898A>T K [AAA] > I [ATA] Coding Sequence Variant
transcription termination factor 2 isoform X3 XP_047288091.1:p.Lys633Ile K (Lys) > I (Ile) Missense Variant
TTF2 transcript variant X5 XM_047432136.1:c.1898A>T K [AAA] > I [ATA] Coding Sequence Variant
transcription termination factor 2 isoform X3 XP_047288092.1:p.Lys633Ile K (Lys) > I (Ile) Missense Variant
TTF2 transcript variant X6 XM_047432139.1:c.1895A>T K [AAA] > I [ATA] Coding Sequence Variant
transcription termination factor 2 isoform X4 XP_047288095.1:p.Lys632Ile K (Lys) > I (Ile) Missense Variant
TTF2 transcript variant X7 XM_047432141.1:c.1919A>T K [AAA] > I [ATA] Coding Sequence Variant
transcription termination factor 2 isoform X5 XP_047288097.1:p.Lys640Ile K (Lys) > I (Ile) Missense Variant
TTF2 transcript variant X8 XM_047432143.1:c.1919A>T K [AAA] > I [ATA] Coding Sequence Variant
transcription termination factor 2 isoform X5 XP_047288099.1:p.Lys640Ile K (Lys) > I (Ile) Missense Variant
TTF2 transcript variant X9 XM_047432144.1:c.1916A>T K [AAA] > I [ATA] Coding Sequence Variant
transcription termination factor 2 isoform X6 XP_047288100.1:p.Lys639Ile K (Lys) > I (Ile) Missense Variant
TTF2 transcript variant X10 XM_047432147.1:c.1916A>T K [AAA] > I [ATA] Coding Sequence Variant
transcription termination factor 2 isoform X6 XP_047288103.1:p.Lys639Ile K (Lys) > I (Ile) Missense Variant
TTF2 transcript variant X11 XM_017002555.3:c.1898A>T K [AAA] > I [ATA] Coding Sequence Variant
transcription termination factor 2 isoform X7 XP_016858044.1:p.Lys633Ile K (Lys) > I (Ile) Missense Variant
TTF2 transcript variant X12 XM_047432152.1:c.1898A>T K [AAA] > I [ATA] Coding Sequence Variant
transcription termination factor 2 isoform X7 XP_047288108.1:p.Lys633Ile K (Lys) > I (Ile) Missense Variant
TTF2 transcript variant X13 XM_047432155.1:c.1895A>T K [AAA] > I [ATA] Coding Sequence Variant
transcription termination factor 2 isoform X8 XP_047288111.1:p.Lys632Ile K (Lys) > I (Ile) Missense Variant
TTF2 transcript variant X14 XM_047432157.1:c.1895A>T K [AAA] > I [ATA] Coding Sequence Variant
transcription termination factor 2 isoform X8 XP_047288113.1:p.Lys632Ile K (Lys) > I (Ile) Missense Variant
TTF2 transcript variant X16 XM_047432161.1:c.1919A>T K [AAA] > I [ATA] Coding Sequence Variant
transcription termination factor 2 isoform X9 XP_047288117.1:p.Lys640Ile K (Lys) > I (Ile) Missense Variant
TTF2 transcript variant X19 XM_047432162.1:c.1898A>T K [AAA] > I [ATA] Coding Sequence Variant
transcription termination factor 2 isoform X10 XP_047288118.1:p.Lys633Ile K (Lys) > I (Ile) Missense Variant
TTF2 transcript variant X15 XR_007064424.1:n.1940A>T N/A Non Coding Transcript Variant
TTF2 transcript variant X17 XR_007064425.1:n.1940A>T N/A Non Coding Transcript Variant
TTF2 transcript variant X18 XR_007064426.1:n.1919A>T N/A Non Coding Transcript Variant
TTF2 transcript variant X20 XR_007064427.1:n.1940A>T N/A Non Coding Transcript Variant
TTF2 transcript variant X21 XR_007064429.1:n.1919A>T N/A Non Coding 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 A= T
GRCh38.p14 chr 1 NC_000001.11:g.117081942= NC_000001.11:g.117081942A>T
GRCh37.p13 chr 1 NC_000001.10:g.117624564= NC_000001.10:g.117624564A>T
TTF2 transcript NM_003594.4:c.1898= NM_003594.4:c.1898A>T
TTF2 transcript NM_003594.3:c.1898= NM_003594.3:c.1898A>T
TTF2 transcript variant X3 XM_017002552.3:c.1916= XM_017002552.3:c.1916A>T
TTF2 transcript variant X3 XM_017002552.2:c.1916= XM_017002552.2:c.1916A>T
TTF2 transcript variant X4 XM_017002552.1:c.1916= XM_017002552.1:c.1916A>T
TTF2 transcript variant X1 XM_017002550.3:c.1919= XM_017002550.3:c.1919A>T
TTF2 transcript variant X1 XM_017002550.2:c.1919= XM_017002550.2:c.1919A>T
TTF2 transcript variant X2 XM_017002550.1:c.1919= XM_017002550.1:c.1919A>T
TTF2 transcript variant X2 XM_017002551.3:c.1919= XM_017002551.3:c.1919A>T
TTF2 transcript variant X2 XM_017002551.2:c.1919= XM_017002551.2:c.1919A>T
TTF2 transcript variant X3 XM_017002551.1:c.1919= XM_017002551.1:c.1919A>T
TTF2 transcript variant X11 XM_017002555.3:c.1898= XM_017002555.3:c.1898A>T
TTF2 transcript variant X7 XM_017002555.2:c.1898= XM_017002555.2:c.1898A>T
TTF2 transcript variant X8 XM_017002555.1:c.1898= XM_017002555.1:c.1898A>T
TTF2 transcript variant X4 XM_047432135.1:c.1898= XM_047432135.1:c.1898A>T
TTF2 transcript variant X7 XM_047432141.1:c.1919= XM_047432141.1:c.1919A>T
TTF2 transcript variant X9 XM_047432144.1:c.1916= XM_047432144.1:c.1916A>T
TTF2 transcript variant X15 XR_007064424.1:n.1940= XR_007064424.1:n.1940A>T
TTF2 transcript variant X13 XM_047432155.1:c.1895= XM_047432155.1:c.1895A>T
TTF2 transcript variant X5 XM_047432136.1:c.1898= XM_047432136.1:c.1898A>T
TTF2 transcript variant X6 XM_047432139.1:c.1895= XM_047432139.1:c.1895A>T
TTF2 transcript variant X17 XR_007064425.1:n.1940= XR_007064425.1:n.1940A>T
TTF2 transcript variant X8 XM_047432143.1:c.1919= XM_047432143.1:c.1919A>T
TTF2 transcript variant X10 XM_047432147.1:c.1916= XM_047432147.1:c.1916A>T
TTF2 transcript variant X18 XR_007064426.1:n.1919= XR_007064426.1:n.1919A>T
TTF2 transcript variant X12 XM_047432152.1:c.1898= XM_047432152.1:c.1898A>T
TTF2 transcript variant X14 XM_047432157.1:c.1895= XM_047432157.1:c.1895A>T
TTF2 transcript variant X16 XM_047432161.1:c.1919= XM_047432161.1:c.1919A>T
TTF2 transcript variant X19 XM_047432162.1:c.1898= XM_047432162.1:c.1898A>T
TTF2 transcript variant X20 XR_007064427.1:n.1940= XR_007064427.1:n.1940A>T
TTF2 transcript variant X21 XR_007064429.1:n.1919= XR_007064429.1:n.1919A>T
transcription termination factor 2 NP_003585.3:p.Lys633= NP_003585.3:p.Lys633Ile
transcription termination factor 2 isoform X2 XP_016858041.1:p.Lys639= XP_016858041.1:p.Lys639Ile
transcription termination factor 2 isoform X1 XP_016858039.1:p.Lys640= XP_016858039.1:p.Lys640Ile
transcription termination factor 2 isoform X1 XP_016858040.1:p.Lys640= XP_016858040.1:p.Lys640Ile
transcription termination factor 2 isoform X7 XP_016858044.1:p.Lys633= XP_016858044.1:p.Lys633Ile
transcription termination factor 2 isoform X3 XP_047288091.1:p.Lys633= XP_047288091.1:p.Lys633Ile
transcription termination factor 2 isoform X5 XP_047288097.1:p.Lys640= XP_047288097.1:p.Lys640Ile
transcription termination factor 2 isoform X6 XP_047288100.1:p.Lys639= XP_047288100.1:p.Lys639Ile
transcription termination factor 2 isoform X8 XP_047288111.1:p.Lys632= XP_047288111.1:p.Lys632Ile
transcription termination factor 2 isoform X3 XP_047288092.1:p.Lys633= XP_047288092.1:p.Lys633Ile
transcription termination factor 2 isoform X4 XP_047288095.1:p.Lys632= XP_047288095.1:p.Lys632Ile
transcription termination factor 2 isoform X5 XP_047288099.1:p.Lys640= XP_047288099.1:p.Lys640Ile
transcription termination factor 2 isoform X6 XP_047288103.1:p.Lys639= XP_047288103.1:p.Lys639Ile
transcription termination factor 2 isoform X7 XP_047288108.1:p.Lys633= XP_047288108.1:p.Lys633Ile
transcription termination factor 2 isoform X8 XP_047288113.1:p.Lys632= XP_047288113.1:p.Lys632Ile
transcription termination factor 2 isoform X9 XP_047288117.1:p.Lys640= XP_047288117.1:p.Lys640Ile
transcription termination factor 2 isoform X10 XP_047288118.1:p.Lys633= XP_047288118.1:p.Lys633Ile
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#.

2 SubSNP, 3 Frequency submissions
No Submitter Submission ID Date (Build)
1 GNOMAD ss4001136091 Apr 25, 2021 (155)
2 TOPMED ss4465032350 Apr 25, 2021 (155)
3 gnomAD - Genomes NC_000001.11 - 117081942 Apr 25, 2021 (155)
4 TopMed NC_000001.11 - 117081942 Apr 25, 2021 (155)
5 ALFA NC_000001.11 - 117081942 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
23855466, 28638685, 1838186672, ss4001136091, ss4465032350 NC_000001.11:117081941:A:T NC_000001.11:117081941:A: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 rs1484862538

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