Genetic Variant PDGFC:p.Gly344Gly (chr4-156763096-T-C) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_016205.3(PDGFC):c.1032A>G(p.Gly344Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.169 in 1,567,192 control chromosomes in the GnomAD database, including 25,106 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 0.18 ( 2520 hom., cov: 31)

Exomes 𝑓: 0.17 ( 22586 hom. )

Consequence

PDGFC
NM_016205.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.339

Publications

15 publications found

Variant links:

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 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.62).

BP7

Synonymous conserved (PhyloP=0.339 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.385 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PDGFC	NM_016205.3 link	c.1032A>G	p.Gly344Gly	synonymous_variant	Exon 6 of 6	ENST00000502773.6	NP_057289.1	Q9NRA1-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PDGFC	ENST00000502773.6 link	c.1032A>G	p.Gly344Gly	synonymous_variant	Exon 6 of 6	1	NM_016205.3	ENSP00000422464.1		Q9NRA1-1

Frequencies

GnomAD3 genomes

AF:

0.176

AC:

26794

AN:

151910

Hom.:

2520

Cov.:

show subpopulations

Gnomad AFR

AF:

0.204

Gnomad AMI

AF:

0.0859

Gnomad AMR

AF:

0.160

Gnomad ASJ

AF:

0.133

Gnomad EAS

AF:

0.164

Gnomad SAS

AF:

0.401

Gnomad FIN

AF:

0.160

Gnomad MID

AF:

0.188

Gnomad NFE

AF:

0.155

Gnomad OTH

AF:

0.166

GnomAD2 exomes

AF:

0.194

AC:

48620

AN:

250764

AF XY:

0.202

show subpopulations

Gnomad AFR exome

AF:

0.197

Gnomad AMR exome

AF:

0.203

Gnomad ASJ exome

AF:

0.137

Gnomad EAS exome

AF:

0.172

Gnomad FIN exome

AF:

0.161

Gnomad NFE exome

AF:

0.153

Gnomad OTH exome

AF:

0.184

GnomAD4 exome

AF:

0.168

AC:

237480

AN:

1415164

Hom.:

22586

Cov.:

AF XY:

0.174

AC XY:

123281

AN XY:

706936

show subpopulations

African (AFR)

AF:

0.199

AC:

6464

AN:

32468

American (AMR)

AF:

0.196

AC:

8741

AN:

44666

Ashkenazi Jewish (ASJ)

AF:

0.139

AC:

3593

AN:

25836

East Asian (EAS)

AF:

0.179

AC:

7055

AN:

39500

South Asian (SAS)

AF:

0.383

AC:

32590

AN:

85156

European-Finnish (FIN)

AF:

0.160

AC:

8561

AN:

53382

Middle Eastern (MID)

AF:

0.217

AC:

1228

AN:

5656

European-Non Finnish (NFE)

AF:

0.149

AC:

159387

AN:

1069688

Other (OTH)

AF:

0.168

AC:

9861

AN:

58812

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.484

Heterozygous variant carriers

9045

18090

27135

36180

45225

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.176

AC:

26806

AN:

152028

Hom.:

2520

Cov.:

AF XY:

0.180

AC XY:

13380

AN XY:

74304

show subpopulations

African (AFR)

AF:

0.204

AC:

8453

AN:

41478

American (AMR)

AF:

0.160

AC:

2441

AN:

15264

Ashkenazi Jewish (ASJ)

AF:

0.133

AC:

461

AN:

3470

East Asian (EAS)

AF:

0.163

AC:

842

AN:

5150

South Asian (SAS)

AF:

0.400

AC:

1928

AN:

4816

European-Finnish (FIN)

AF:

0.160

AC:

1693

AN:

10570

Middle Eastern (MID)

AF:

0.185

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.155

AC:

10505

AN:

67972

Other (OTH)

AF:

0.167

AC:

351

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1108

2216

3323

4431

5539

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.149

Hom.:

1409

Bravo

AF:

0.172

Asia WGS

AF:

0.274

AC:

950

AN:

3478

EpiCase

AF:

0.155

EpiControl

AF:

0.157

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.62

CADD

Benign

7.8

(source)

DANN

Benign

0.69

PhyloP100

0.34

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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4-156763096-T-C

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over