4-54264959-C-T
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_ModerateBP6_Very_StrongBP7BS2
The NM_006206.6(PDGFRA):c.669C>T(p.Thr223Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000107 in 1,612,984 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 (★★). Synonymous variant affecting the same amino acid position (i.e. T223T) has been classified as Likely benign.
Frequency
Consequence
NM_006206.6 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PDGFRA | ENST00000257290.10 | c.669C>T | p.Thr223Thr | synonymous_variant | Exon 5 of 23 | 1 | NM_006206.6 | ENSP00000257290.5 | ||
ENSG00000282278 | ENST00000507166.5 | c.1018-9966C>T | intron_variant | Intron 12 of 23 | 2 | ENSP00000423325.1 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 151858Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000795 AC: 20AN: 251436Hom.: 0 AF XY: 0.0000957 AC XY: 13AN XY: 135886
GnomAD4 exome AF: 0.000114 AC: 166AN: 1461012Hom.: 0 Cov.: 31 AF XY: 0.000111 AC XY: 81AN XY: 726896
GnomAD4 genome AF: 0.0000395 AC: 6AN: 151972Hom.: 0 Cov.: 32 AF XY: 0.0000539 AC XY: 4AN XY: 74274
ClinVar
Submissions by phenotype
Gastrointestinal stromal tumor Benign:1
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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