4-54657917-C-CCGCTCGCGGCTCTGGGGGCTCGGCTTTGCCGCGCTCGCTGCACTTGGGCGAGAGCTGGAACGTGGACCAGAGCTCGGATCCCATCGCAGCTACCGCGATGAGAGG
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PM4
The ENST00000288135.6(KIT):c.-87_18dupTCTGGGGGCTCGGCTTTGCCGCGCTCGCTGCACTTGGGCGAGAGCTGGAACGTGGACCAGAGCTCGGATCCCATCGCAGCTACCGCGATGAGAGGCGCTCGCGGC(p.Gly6_Ala7insSerGlyGlySerAlaLeuProArgSerLeuHisLeuGlyGluSerTrpAsnValAspGlnSerSerAspProIleAlaAlaThrAlaMetArgGlyAlaArgGly) variant causes a conservative inframe insertion change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. A7A) has been classified as Likely benign.
Frequency
Consequence
ENST00000288135.6 conservative_inframe_insertion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KIT | ENST00000288135.6 | c.-87_18dupTCTGGGGGCTCGGCTTTGCCGCGCTCGCTGCACTTGGGCGAGAGCTGGAACGTGGACCAGAGCTCGGATCCCATCGCAGCTACCGCGATGAGAGGCGCTCGCGGC | p.Gly6_Ala7insSerGlyGlySerAlaLeuProArgSerLeuHisLeuGlyGluSerTrpAsnValAspGlnSerSerAspProIleAlaAlaThrAlaMetArgGlyAlaArgGly | conservative_inframe_insertion | Exon 1 of 21 | 1 | NM_000222.3 | ENSP00000288135.6 | ||
KIT | ENST00000288135.6 | c.-98_-97insCGCTCGCGGCTCTGGGGGCTCGGCTTTGCCGCGCTCGCTGCACTTGGGCGAGAGCTGGAACGTGGACCAGAGCTCGGATCCCATCGCAGCTACCGCGATGAGAGG | upstream_gene_variant | 1 | NM_000222.3 | ENSP00000288135.6 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 15
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Gastrointestinal stromal tumor Uncertain:1
This variant occurs in a non-coding region of the KIT gene. It does not change the encoded amino acid sequence of the KIT protein. This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with KIT-related conditions. This variant is also known as p.Gly6_Ala7ins35. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.