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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.

rs1057520035

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr4:54727438-54727439 (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
GG>TT
Variation Type
MNV Multiple Nucleotide Variation
Frequency
None
Clinical Significance
Reported in ClinVar
Gene : Consequence
KIT : Missense Variant
Publications
1 citation
Genomic View
See rs on genome
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").

None
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 4 NC_000004.12:g.54727438_54727439delinsTT
GRCh37.p13 chr 4 NC_000004.11:g.55593604_55593605delinsTT
KIT RefSeqGene (LRG_307) NG_007456.1:g.74444_74445delinsTT
Gene: KIT, KIT proto-oncogene, receptor tyrosine kinase (plus strand)
Molecule type Change Amino acid[Codon] SO Term
KIT transcript variant 1 NM_000222.3:c.1670_1671de…

NM_000222.3:c.1670_1671delinsTT

W [TGG] > F [TTT] Coding Sequence Variant
mast/stem cell growth factor receptor Kit isoform 1 precursor NP_000213.1:p.Trp557Phe W (Trp) > F (Phe) Missense Variant
KIT transcript variant 7 NM_001385290.1:c.1673_167…

NM_001385290.1:c.1673_1674delinsTT

W [TGG] > F [TTT] Coding Sequence Variant
mast/stem cell growth factor receptor Kit isoform 7 precursor NP_001372219.1:p.Trp558Phe W (Trp) > F (Phe) Missense Variant
KIT transcript variant 4 NM_001385285.1:c.1670_167…

NM_001385285.1:c.1670_1671delinsTT

W [TGG] > F [TTT] Coding Sequence Variant
mast/stem cell growth factor receptor Kit isoform 4 precursor NP_001372214.1:p.Trp557Phe W (Trp) > F (Phe) Missense Variant
KIT transcript variant 3 NM_001385284.1:c.1673_167…

NM_001385284.1:c.1673_1674delinsTT

W [TGG] > F [TTT] Coding Sequence Variant
mast/stem cell growth factor receptor Kit isoform 3 precursor NP_001372213.1:p.Trp558Phe W (Trp) > F (Phe) Missense Variant
KIT transcript variant 2 NM_001093772.2:c.1658_165…

NM_001093772.2:c.1658_1659delinsTT

W [TGG] > F [TTT] Coding Sequence Variant
mast/stem cell growth factor receptor Kit isoform 2 precursor NP_001087241.1:p.Trp553Phe W (Trp) > F (Phe) Missense Variant
KIT transcript variant 6 NM_001385288.1:c.1661_166…

NM_001385288.1:c.1661_1662delinsTT

W [TGG] > F [TTT] Coding Sequence Variant
mast/stem cell growth factor receptor Kit isoform 6 precursor NP_001372217.1:p.Trp554Phe W (Trp) > F (Phe) Missense Variant
KIT transcript variant 8 NM_001385292.1:c.1661_166…

NM_001385292.1:c.1661_1662delinsTT

W [TGG] > F [TTT] Coding Sequence Variant
mast/stem cell growth factor receptor Kit isoform 8 precursor NP_001372221.1:p.Trp554Phe W (Trp) > F (Phe) Missense Variant
KIT transcript variant 5 NM_001385286.1:c.1658_165…

NM_001385286.1:c.1658_1659delinsTT

W [TGG] > F [TTT] Coding Sequence Variant
mast/stem cell growth factor receptor Kit isoform 5 precursor NP_001372215.1:p.Trp553Phe W (Trp) > F (Phe) Missense 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.

Allele: TT (allele ID: 363615 )
ClinVar Accession Disease Names Clinical Significance
RCV000428828.1 Gastrointestinal stromal tumor Likely-Pathogenic
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 GG= TT
GRCh38.p14 chr 4 NC_000004.12:g.54727438_54727439= NC_000004.12:g.54727438_54727439delinsTT
GRCh37.p13 chr 4 NC_000004.11:g.55593604_55593605= NC_000004.11:g.55593604_55593605delinsTT
KIT RefSeqGene (LRG_307) NG_007456.1:g.74444_74445= NG_007456.1:g.74444_74445delinsTT
KIT transcript variant 1 NM_000222.3:c.1670_1671= NM_000222.3:c.1670_1671delinsTT
KIT transcript variant 1 NM_000222.2:c.1670_1671= NM_000222.2:c.1670_1671delinsTT
KIT transcript variant 2 NM_001093772.2:c.1658_1659= NM_001093772.2:c.1658_1659delinsTT
KIT transcript variant 2 NM_001093772.1:c.1658_1659= NM_001093772.1:c.1658_1659delinsTT
KIT transcript variant 3 NM_001385284.1:c.1673_1674= NM_001385284.1:c.1673_1674delinsTT
KIT transcript variant 7 NM_001385290.1:c.1673_1674= NM_001385290.1:c.1673_1674delinsTT
KIT transcript variant 4 NM_001385285.1:c.1670_1671= NM_001385285.1:c.1670_1671delinsTT
KIT transcript variant 6 NM_001385288.1:c.1661_1662= NM_001385288.1:c.1661_1662delinsTT
KIT transcript variant 8 NM_001385292.1:c.1661_1662= NM_001385292.1:c.1661_1662delinsTT
KIT transcript variant 5 NM_001385286.1:c.1658_1659= NM_001385286.1:c.1658_1659delinsTT
mast/stem cell growth factor receptor Kit isoform 1 precursor NP_000213.1:p.Trp557= NP_000213.1:p.Trp557Phe
mast/stem cell growth factor receptor Kit isoform 2 precursor NP_001087241.1:p.Trp553= NP_001087241.1:p.Trp553Phe
mast/stem cell growth factor receptor Kit isoform 3 precursor NP_001372213.1:p.Trp558= NP_001372213.1:p.Trp558Phe
mast/stem cell growth factor receptor Kit isoform 7 precursor NP_001372219.1:p.Trp558= NP_001372219.1:p.Trp558Phe
mast/stem cell growth factor receptor Kit isoform 4 precursor NP_001372214.1:p.Trp557= NP_001372214.1:p.Trp557Phe
mast/stem cell growth factor receptor Kit isoform 6 precursor NP_001372217.1:p.Trp554= NP_001372217.1:p.Trp554Phe
mast/stem cell growth factor receptor Kit isoform 8 precursor NP_001372221.1:p.Trp554= NP_001372221.1:p.Trp554Phe
mast/stem cell growth factor receptor Kit isoform 5 precursor NP_001372215.1:p.Trp553= NP_001372215.1:p.Trp553Phe
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, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 CLINVAR ss2137498528 Apr 13, 2017 (150)
2 CLINVAR ss2137504919 Apr 18, 2017 (150)
3 ClinVar RCV000428828.1 Oct 12, 2018 (152)
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
RCV000428828.1, ss2137498528, ss2137504919 NC_000004.12:54727437:GG:TT NC_000004.12:54727437:GG:TT (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

1 citation for rs1057520035
PMID Title Author Year Journal
16731599 An update on molecular genetics of gastrointestinal stromal tumours. Tornillo L et al. 2006 Journal of clinical pathology
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.post761+d5e8e07