rs17035464

chr4-156958569-T-A

Variant summary

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

The NM_016205.3(PDGFC):c.118+12217A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0866 in 152,068 control chromosomes in the GnomAD database, including 1,682 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 0.087 (1682 hom., cov: 32)
• Consequence: PDGFC NM_016205.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.376

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.277 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PDGFC	NM_016205.3	c.118+12217A>T		intron_variant		ENST00000502773.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PDGFC	ENST00000502773.6	c.118+12217A>T		intron_variant		1	NM_016205.3	P1
PDGFC	ENST00000274071.6	c.118+12217A>T		intron_variant, NMD_transcript_variant		1
PDGFC	ENST00000422544.2	c.118+12217A>T		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.0862 AC: 13099 AN: 151950 Hom.: 1667 Cov.: 32

Gnomad AFR AF: 0.280

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0332

Gnomad ASJ AF: 0.00490

Gnomad EAS AF: 0.102

Gnomad SAS AF: 0.0263

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.00275

Gnomad OTH AF: 0.0664

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

GnomAD4 genome AF: 0.0866 AC: 13162 AN: 152068 Hom.: 1682 Cov.: 32 AF XY: 0.0852 AC XY: 6335 AN XY: 74334

Gnomad4 AFR AF: 0.281

Gnomad4 AMR AF: 0.0331

Gnomad4 ASJ AF: 0.00490

Gnomad4 EAS AF: 0.102

Gnomad4 SAS AF: 0.0259

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00275

Gnomad4 OTH AF: 0.0658

Alfa AF: 0.0659 Hom.: 122

Bravo AF: 0.0989

Asia WGS AF: 0.0800 AC: 277 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	8.7
Dann	Benign	0.54

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: rs17035464; hg19: chr4-157879721;