rs3733486
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_016205.3(PDGFC):c.-379C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00952 in 424,826 control chromosomes in the GnomAD database, including 250 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0043 ( 21 hom., cov: 31)
Exomes 𝑓: 0.012 ( 229 hom. )
Consequence
PDGFC
NM_016205.3 5_prime_UTR
NM_016205.3 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.577
Genes affected
PDGFC (HGNC:8801): (platelet derived growth factor C) The protein encoded by this gene is a member of the platelet-derived growth factor family. The four members of this family are mitogenic factors for cells of mesenchymal origin and are characterized by a core motif of eight cysteines. This gene product appears to form only homodimers. It differs from the platelet-derived growth factor alpha and beta polypeptides in having an unusual N-terminal domain, the CUB domain. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Sep 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.68).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0914 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PDGFC | NM_016205.3 | c.-379C>T | 5_prime_UTR_variant | 1/6 | ENST00000502773.6 | ||
PDGFC | NR_036641.2 | n.518C>T | non_coding_transcript_exon_variant | 1/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PDGFC | ENST00000502773.6 | c.-379C>T | 5_prime_UTR_variant | 1/6 | 1 | NM_016205.3 | P1 | ||
PDGFC | ENST00000274071.6 | c.-379C>T | 5_prime_UTR_variant, NMD_transcript_variant | 1/7 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.00432 AC: 656AN: 151930Hom.: 21 Cov.: 31
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GnomAD4 exome AF: 0.0124 AC: 3392AN: 272786Hom.: 229 Cov.: 0 AF XY: 0.0120 AC XY: 1665AN XY: 138656
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GnomAD4 genome ? AF: 0.00429 AC: 652AN: 152040Hom.: 21 Cov.: 31 AF XY: 0.00464 AC XY: 345AN XY: 74292
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at