chr4-54731899-C-T
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_000222.3(KIT):c.2262C>T(p.Pro754Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000384 in 1,613,564 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_000222.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000789 AC: 12AN: 152016Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000915 AC: 23AN: 251330Hom.: 0 AF XY: 0.0000736 AC XY: 10AN XY: 135830
GnomAD4 exome AF: 0.0000342 AC: 50AN: 1461430Hom.: 0 Cov.: 34 AF XY: 0.0000371 AC XY: 27AN XY: 727026
GnomAD4 genome AF: 0.0000789 AC: 12AN: 152134Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74382
ClinVar
Submissions by phenotype
Gastrointestinal stromal tumor Benign:2
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Hereditary cancer-predisposing syndrome Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at