rs11728198

chr4-156904245-G-A

Variant summary

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

The NM_016205.3(PDGFC):c.119-53829C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.6 in 151,754 control chromosomes in the GnomAD database, including 27,470 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 0.60 (27470 hom., cov: 31)
• Consequence: PDGFC NM_016205.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.377

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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.677 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PDGFC	NM_016205.3	c.119-53829C>T		intron_variant		ENST00000502773.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PDGFC	ENST00000502773.6	c.119-53829C>T		intron_variant		1	NM_016205.3	P1
PDGFC	ENST00000274071.6	c.119-42756C>T		intron_variant, NMD_transcript_variant		1
PDGFC	ENST00000422544.2	c.119-53829C>T		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.600 AC: 90915 AN: 151636 Hom.: 27439 Cov.: 31

Gnomad AFR AF: 0.605

Gnomad AMI AF: 0.500

Gnomad AMR AF: 0.649

Gnomad ASJ AF: 0.460

Gnomad EAS AF: 0.697

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.652

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.594

Gnomad OTH AF: 0.599

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

GnomAD4 genome AF: 0.600 AC: 91009 AN: 151754 Hom.: 27470 Cov.: 31 AF XY: 0.601 AC XY: 44571 AN XY: 74142

Gnomad4 AFR AF: 0.605

Gnomad4 AMR AF: 0.650

Gnomad4 ASJ AF: 0.460

Gnomad4 EAS AF: 0.697

Gnomad4 SAS AF: 0.374

Gnomad4 FIN AF: 0.652

Gnomad4 NFE AF: 0.594

Gnomad4 OTH AF: 0.599

Alfa AF: 0.585 Hom.: 47505

Bravo AF: 0.601

Asia WGS AF: 0.541 AC: 1883 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	1.5
Dann	Benign	0.42

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: rs11728198; hg19: chr4-157825397;