4-54280424-C-G
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The ENST00000257290.10(PDGFRA):āc.2265C>Gā(p.Ser755=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000205 in 1,461,300 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 (ā ). Synonymous variant affecting the same amino acid position (i.e. S755S) has been classified as Likely benign.
Frequency
Consequence
ENST00000257290.10 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PDGFRA | NM_006206.6 | c.2265C>G | p.Ser755= | synonymous_variant | 16/23 | ENST00000257290.10 | NP_006197.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PDGFRA | ENST00000257290.10 | c.2265C>G | p.Ser755= | synonymous_variant | 16/23 | 1 | NM_006206.6 | ENSP00000257290 | P1 | |
PDGFRA | ENST00000507536.1 | n.691C>G | non_coding_transcript_exon_variant | 4/5 | 1 | |||||
PDGFRA | ENST00000509092.5 | n.2083C>G | non_coding_transcript_exon_variant | 15/15 | 1 | |||||
PDGFRA | ENST00000509490.5 | c.*186C>G | 3_prime_UTR_variant, NMD_transcript_variant | 17/18 | 1 | ENSP00000424218 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251070Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135684
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461300Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 726978
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Gastrointestinal stromal tumor Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | May 24, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at