4-156970811-C-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_016205.3(PDGFC):c.93G>T(p.Gln31His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00396 in 1,611,858 control chromosomes in the GnomAD database, including 16 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. Q31R) has been classified as Uncertain significance.
Frequency
Consequence
NM_016205.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PDGFC | ENST00000502773.6 | c.93G>T | p.Gln31His | missense_variant | Exon 1 of 6 | 1 | NM_016205.3 | ENSP00000422464.1 | ||
PDGFC | ENST00000274071.6 | n.93G>T | non_coding_transcript_exon_variant | Exon 1 of 7 | 1 | ENSP00000274071.2 | ||||
PDGFC | ENST00000422544.2 | c.93G>T | p.Gln31His | missense_variant | Exon 1 of 6 | 5 | ENSP00000410048.2 | |||
PDGFC | ENST00000513664.1 | n.155G>T | non_coding_transcript_exon_variant | Exon 1 of 2 | 3 |
Frequencies
GnomAD3 genomes AF: 0.00309 AC: 470AN: 152162Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.00276 AC: 693AN: 251442Hom.: 1 AF XY: 0.00269 AC XY: 365AN XY: 135908
GnomAD4 exome AF: 0.00405 AC: 5914AN: 1459578Hom.: 15 Cov.: 30 AF XY: 0.00408 AC XY: 2965AN XY: 726286
GnomAD4 genome AF: 0.00309 AC: 470AN: 152280Hom.: 1 Cov.: 32 AF XY: 0.00271 AC XY: 202AN XY: 74432
ClinVar
Submissions by phenotype
PDGFC-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
not provided Benign:1
PDGFC: BP4, BS2 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at