dbSNP rs1425486: PDGFC:n.*1503G>A (chr4-156762533-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000274071.6(PDGFC):n.*1503G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.46 in 151,456 control chromosomes in the GnomAD database, including 19,122 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 0.46 ( 19122 hom., cov: 30)

Exomes 𝑓: 0.30 ( 0 hom. )

Consequence

PDGFC
ENST00000274071.6 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0370

Publications

31 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:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.763 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PDGFC	NM_016205.3 link	c.*557G>A		3_prime_UTR_variant	Exon 6 of 6	ENST00000502773.6	NP_057289.1	Q9NRA1-1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
PDGFC	ENST00000274071.6 link	n.*1503G>A	non_coding_transcript_exon_variant	Exon 7 of 7	1		ENSP00000274071.2	J3KN71
PDGFC	ENST00000502773.6 link	c.*557G>A	3_prime_UTR_variant	Exon 6 of 6	1	NM_016205.3	ENSP00000422464.1	Q9NRA1-1
PDGFC	ENST00000274071.6 link	n.*1503G>A	3_prime_UTR_variant	Exon 7 of 7	1		ENSP00000274071.2	J3KN71

Frequencies

GnomAD3 genomes

AF:

0.460

AC:

69538

AN:

151288

Hom.:

19073

Cov.:

show subpopulations

Gnomad AFR

AF:

0.770

Gnomad AMI

AF:

0.360

Gnomad AMR

AF:

0.370

Gnomad ASJ

AF:

0.430

Gnomad EAS

AF:

0.290

Gnomad SAS

AF:

0.612

Gnomad FIN

AF:

0.261

Gnomad MID

AF:

0.494

Gnomad NFE

AF:

0.327

Gnomad OTH

AF:

0.452

GnomAD4 exome

AF:

0.304

AC:

AN:

Hom.:

Cov.:

AF XY:

0.357

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AF:

0.500

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.265

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.400

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.460

AC:

69643

AN:

151410

Hom.:

19122

Cov.:

AF XY:

0.458

AC XY:

33819

AN XY:

73892

show subpopulations

African (AFR)

AF:

0.770

AC:

31836

AN:

41334

American (AMR)

AF:

0.370

AC:

5614

AN:

15178

Ashkenazi Jewish (ASJ)

AF:

0.430

AC:

1490

AN:

3462

East Asian (EAS)

AF:

0.290

AC:

1490

AN:

5138

South Asian (SAS)

AF:

0.612

AC:

2942

AN:

4804

European-Finnish (FIN)

AF:

0.261

AC:

2693

AN:

10328

Middle Eastern (MID)

AF:

0.490

AC:

142

AN:

290

European-Non Finnish (NFE)

AF:

0.326

AC:

22155

AN:

67858

Other (OTH)

AF:

0.452

AC:

953

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1575

3149

4724

6298

7873

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

614

1228

1842

2456

3070

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.374

Hom.:

12580

Bravo

AF:

0.478

Asia WGS

AF:

0.487

AC:

1690

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

3.0

(source)

DANN

Benign

0.62

PhyloP100

-0.037

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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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