rs342318

Variant names:

• chr4-156867803-G-A
• rs342318
• NM_016205.3:c.119-17387C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_016205.3(PDGFC):​c.119-17387C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.221 in 152,060 control chromosomes in the GnomAD database, including 4,467 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 0.22 (4467 hom., cov: 32)
• Consequence: PDGFC NM_016205.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.516 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PDGFC	NM_016205.3	c.119-17387C>T		intron_variant	Intron 1 of 5	ENST00000502773.6	NP_057289.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PDGFC	ENST00000502773.6	c.119-17387C>T		intron_variant	Intron 1 of 5	1	NM_016205.3	ENSP00000422464.1
PDGFC	ENST00000274071.6	n.119-6314C>T		intron_variant	Intron 1 of 6	1		ENSP00000274071.2
PDGFC	ENST00000422544.2	c.119-17387C>T		intron_variant	Intron 1 of 5	5		ENSP00000410048.2
PDGFC	ENST00000512711.1	n.67+6103C>T		intron_variant	Intron 1 of 4	3

Frequencies

GnomAD3 genomes AF: 0.221 AC: 33560 AN: 151942 Hom.: 4448 Cov.: 32

Gnomad AFR AF: 0.328

Gnomad AMI AF: 0.0987

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.238

Gnomad SAS AF: 0.534

Gnomad FIN AF: 0.0800

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.216

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

GnomAD4 genome AF: 0.221 AC: 33619 AN: 152060 Hom.: 4467 Cov.: 32 AF XY: 0.223 AC XY: 16557 AN XY: 74354

African (AFR) AF: 0.328 AC: 13599 AN: 41430

American (AMR) AF: 0.221 AC: 3383 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.155 AC: 538 AN: 3470

East Asian (EAS) AF: 0.238 AC: 1226 AN: 5162

South Asian (SAS) AF: 0.534 AC: 2573 AN: 4822

European-Finnish (FIN) AF: 0.0800 AC: 847 AN: 10590

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.159 AC: 10836 AN: 67990

Other (OTH) AF: 0.219 AC: 463 AN: 2112

Alfa AF: 0.192 Hom.: 427

Bravo AF: 0.232

Asia WGS AF: 0.374 AC: 1299 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.64
DANN	Benign	0.65
PhyloP100		-1.2
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs342318; hg19: chr4-157788955;