rs983473

Positions:

• chr4-156774240-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_016205.3(PDGFC):​c.496-1347G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.307 in 152,002 control chromosomes in the GnomAD database, including 8,206 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 0.31 (8205 hom., cov: 32)
  • Exomes 𝑓: 0.17 (1 hom.)
• Consequence: PDGFC NM_016205.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.43

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]

PDGFC (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.53 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PDGFC	NM_016205.3	c.496-1347G>A		intron_variant		ENST00000502773.6	NP_057289.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PDGFC	ENST00000502773.6	c.496-1347G>A		intron_variant		1	NM_016205.3	ENSP00000422464.1

Frequencies

GnomAD3 genomes AF: 0.307 AC: 46606 AN: 151866 Hom.: 8182 Cov.: 32

Gnomad AFR AF: 0.464

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.227

Gnomad EAS AF: 0.221

Gnomad SAS AF: 0.548

Gnomad FIN AF: 0.193

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.295

GnomAD4 exome AF: 0.167 AC: 3 AN: 18 Hom.: 1 AF XY: 0.214 AC XY: 3 AN XY: 14

Gnomad4 NFE exome AF: 0.167

GnomAD4 genome AF: 0.307 AC: 46670 AN: 151984 Hom.: 8205 Cov.: 32 AF XY: 0.307 AC XY: 22843 AN XY: 74288

Gnomad4 AFR AF: 0.464

Gnomad4 AMR AF: 0.274

Gnomad4 ASJ AF: 0.227

Gnomad4 EAS AF: 0.221

Gnomad4 SAS AF: 0.548

Gnomad4 FIN AF: 0.193

Gnomad4 NFE AF: 0.231

Gnomad4 OTH AF: 0.298

Alfa AF: 0.253 Hom.: 6986

Bravo AF: 0.315

Asia WGS AF: 0.408 AC: 1418 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	11
DANN	Benign	0.62

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs983473; hg19: chr4-157695392;