5-150123142-G-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 2P and 8B. PP3_ModerateBS1BS2
The NM_002609.4(PDGFRB):c.2083C>A(p.Arg695Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000093 in 1,613,616 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_002609.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PDGFRB | NM_002609.4 | c.2083C>A | p.Arg695Ser | missense_variant | Exon 15 of 23 | ENST00000261799.9 | NP_002600.1 | |
PDGFRB | NM_001355016.2 | c.1891C>A | p.Arg631Ser | missense_variant | Exon 14 of 22 | NP_001341945.1 | ||
PDGFRB | NM_001355017.2 | c.1600C>A | p.Arg534Ser | missense_variant | Exon 15 of 23 | NP_001341946.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PDGFRB | ENST00000261799.9 | c.2083C>A | p.Arg695Ser | missense_variant | Exon 15 of 23 | 1 | NM_002609.4 | ENSP00000261799.4 | ||
PDGFRB | ENST00000520579.5 | n.*1397C>A | non_coding_transcript_exon_variant | Exon 15 of 23 | 1 | ENSP00000430026.1 | ||||
PDGFRB | ENST00000520579.5 | n.*1397C>A | 3_prime_UTR_variant | Exon 15 of 23 | 1 | ENSP00000430026.1 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152204Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251344Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135860
GnomAD4 exome AF: 0.00000547 AC: 8AN: 1461412Hom.: 0 Cov.: 31 AF XY: 0.00000550 AC XY: 4AN XY: 727060
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152204Hom.: 0 Cov.: 33 AF XY: 0.0000538 AC XY: 4AN XY: 74362
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at