4-156921007-C-T

Variant names:

• chr4-156921007-C-T
• rs7676376
• NM_016205.3:c.118+49779G>A

Variant summary

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

The NM_016205.3(PDGFC):​c.118+49779G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.2 in 151,944 control chromosomes in the GnomAD database, including 3,776 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 0.20 (3776 hom., cov: 32)
• Consequence: PDGFC NM_016205.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.701
• Publications: 6 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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.274 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016205.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PDGFC	NM_016205.3	MANE Select	c.118+49779G>A		intron	N/A	NP_057289.1	Q9NRA1-1
	PDGFC	NR_036641.2		n.1014+49779G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PDGFC	ENST00000502773.6	TSL:1 MANE Select	c.118+49779G>A		intron	N/A	ENSP00000422464.1	Q9NRA1-1
	PDGFC	ENST00000274071.6	TSL:1	n.118+49779G>A		intron	N/A	ENSP00000274071.2	J3KN71
	PDGFC	ENST00000954544.1		c.118+49779G>A		intron	N/A	ENSP00000624603.1

Frequencies

GnomAD3 genomes AF: 0.200 AC: 30438 AN: 151826 Hom.: 3780 Cov.: 32

Gnomad AFR AF: 0.0663

Gnomad AMI AF: 0.454

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.327

Gnomad EAS AF: 0.0125

Gnomad SAS AF: 0.278

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.277

Gnomad OTH AF: 0.197

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

GnomAD4 genome AF: 0.200 AC: 30427 AN: 151944 Hom.: 3776 Cov.: 32 AF XY: 0.198 AC XY: 14722 AN XY: 74240

African (AFR) AF: 0.0662 AC: 2745 AN: 41478

American (AMR) AF: 0.195 AC: 2972 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.327 AC: 1136 AN: 3470

East Asian (EAS) AF: 0.0124 AC: 64 AN: 5168

South Asian (SAS) AF: 0.277 AC: 1331 AN: 4804

European-Finnish (FIN) AF: 0.234 AC: 2463 AN: 10534

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.277 AC: 18834 AN: 67918

Other (OTH) AF: 0.196 AC: 412 AN: 2102

Alfa AF: 0.256 Hom.: 3499

Bravo AF: 0.191

Asia WGS AF: 0.126 AC: 442 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.6
DANN	Benign	0.28
PhyloP100		0.70
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: rs7676376; hg19: chr4-157842159;