chr4-156895991-A-G

Position:

• chr4-156895991-A-G

Variant summary

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

The NM_016205.3(PDGFC):​c.119-45575T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.591 in 151,788 control chromosomes in the GnomAD database, including 26,685 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 0.59 (26685 hom., cov: 31)
• Consequence: PDGFC NM_016205.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.175

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.632 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PDGFC	NM_016205.3	c.119-45575T>C		intron_variant		ENST00000502773.6	NP_057289.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PDGFC	ENST00000502773.6	c.119-45575T>C		intron_variant		1	NM_016205.3	ENSP00000422464.1
PDGFC	ENST00000274071.6	n.119-34502T>C		intron_variant		1		ENSP00000274071.2
PDGFC	ENST00000422544.2	c.119-45575T>C		intron_variant		5		ENSP00000410048.2

Frequencies

GnomAD3 genomes AF: 0.591 AC: 89667 AN: 151666 Hom.: 26666 Cov.: 31

Gnomad AFR AF: 0.596

Gnomad AMI AF: 0.501

Gnomad AMR AF: 0.642

Gnomad ASJ AF: 0.456

Gnomad EAS AF: 0.630

Gnomad SAS AF: 0.356

Gnomad FIN AF: 0.650

Gnomad MID AF: 0.561

Gnomad NFE AF: 0.590

Gnomad OTH AF: 0.590

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

GnomAD4 genome AF: 0.591 AC: 89740 AN: 151788 Hom.: 26685 Cov.: 31 AF XY: 0.592 AC XY: 43883 AN XY: 74124

Gnomad4 AFR AF: 0.596

Gnomad4 AMR AF: 0.642

Gnomad4 ASJ AF: 0.456

Gnomad4 EAS AF: 0.629

Gnomad4 SAS AF: 0.357

Gnomad4 FIN AF: 0.650

Gnomad4 NFE AF: 0.590

Gnomad4 OTH AF: 0.590

Alfa AF: 0.589 Hom.: 3387

Bravo AF: 0.593

Asia WGS AF: 0.497 AC: 1722 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.5
DANN	Benign	0.74

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: rs894588; hg19: chr4-157817143;