rs2113992

chr4-156836603-T-Cchr4-156836603-T-G

Variant summary

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

The NM_016205.3(PDGFC):c.314+13618A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.471 in 152,024 control chromosomes in the GnomAD database, including 20,017 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 0.47 (20017 hom., cov: 32)
• Consequence: PDGFC NM_016205.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.515

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.774 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PDGFC	NM_016205.3	c.314+13618A>G		intron_variant		ENST00000502773.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PDGFC	ENST00000502773.6	c.314+13618A>G		intron_variant		1	NM_016205.3	P1

Frequencies

GnomAD3 genomes AF: 0.471 AC: 71522 AN: 151904 Hom.: 19966 Cov.: 32

Gnomad AFR AF: 0.781

Gnomad AMI AF: 0.374

Gnomad AMR AF: 0.394

Gnomad ASJ AF: 0.417

Gnomad EAS AF: 0.323

Gnomad SAS AF: 0.649

Gnomad FIN AF: 0.258

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.335

Gnomad OTH AF: 0.467

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.471 AC: 71631 AN: 152024 Hom.: 20017 Cov.: 32 AF XY: 0.469 AC XY: 34833 AN XY: 74304

Gnomad4 AFR AF: 0.781

Gnomad4 AMR AF: 0.394

Gnomad4 ASJ AF: 0.417

Gnomad4 EAS AF: 0.323

Gnomad4 SAS AF: 0.649

Gnomad4 FIN AF: 0.258

Gnomad4 NFE AF: 0.335

Gnomad4 OTH AF: 0.468

Alfa AF: 0.319 Hom.: 1517

Bravo AF: 0.492

Asia WGS AF: 0.501 AC: 1735 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.75
Dann	Benign	0.51

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: rs2113992; hg19: chr4-157757755;