11-103943464-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_025208.5(PDGFD):c.760C>T(p.Arg254Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000325 in 1,611,822 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R254Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_025208.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PDGFD | NM_025208.5 | c.760C>T | p.Arg254Trp | missense_variant | 5/7 | ENST00000393158.7 | |
PDGFD | NM_033135.4 | c.742C>T | p.Arg248Trp | missense_variant | 5/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PDGFD | ENST00000393158.7 | c.760C>T | p.Arg254Trp | missense_variant | 5/7 | 1 | NM_025208.5 | P1 | |
PDGFD | ENST00000302251.9 | c.742C>T | p.Arg248Trp | missense_variant | 5/7 | 1 |
Frequencies
GnomAD3 genomes AF: 0.000197 AC: 30AN: 152062Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000112 AC: 28AN: 250260Hom.: 0 AF XY: 0.000118 AC XY: 16AN XY: 135266
GnomAD4 exome AF: 0.000338 AC: 494AN: 1459642Hom.: 0 Cov.: 31 AF XY: 0.000315 AC XY: 229AN XY: 726122
GnomAD4 genome AF: 0.000197 AC: 30AN: 152180Hom.: 0 Cov.: 32 AF XY: 0.000134 AC XY: 10AN XY: 74412
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 01, 2023 | The c.760C>T (p.R254W) alteration is located in exon 5 (coding exon 5) of the PDGFD gene. This alteration results from a C to T substitution at nucleotide position 760, causing the arginine (R) at amino acid position 254 to be replaced by a tryptophan (W). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at