dbSNP rs3733486: PDGFC:c.-379C>T (chr4-156971282-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_016205.3(PDGFC):c.-379C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00952 in 424,826 control chromosomes in the GnomAD database, including 250 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 0.0043 ( 21 hom., cov: 31)

Exomes 𝑓: 0.012 ( 229 hom. )

Consequence

PDGFC
NM_016205.3 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.577

Publications

3 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 -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.68).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0914 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.-379C>T		5_prime_UTR	Exon 1 of 6	NP_057289.1	Q9NRA1-1
	PDGFC	NR_036641.2		n.518C>T		non_coding_transcript_exon	Exon 1 of 7

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
PDGFC	ENST00000502773.6	TSL:1 MANE Select	c.-379C>T	5_prime_UTR	Exon 1 of 6	ENSP00000422464.1	Q9NRA1-1
PDGFC	ENST00000274071.6	TSL:1	n.-379C>T	non_coding_transcript_exon	Exon 1 of 7	ENSP00000274071.2	J3KN71
PDGFC	ENST00000274071.6	TSL:1	n.-379C>T	5_prime_UTR	Exon 1 of 7	ENSP00000274071.2	J3KN71

Frequencies

GnomAD3 genomes

AF:

0.00432

AC:

656

AN:

151930

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00111

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00105

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.0982

Gnomad SAS

AF:

0.00787

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.000648

Gnomad OTH

AF:

0.00335

GnomAD4 exome

AF:

0.0124

AC:

3392

AN:

272786

Hom.:

229

Cov.:

AF XY:

0.0120

AC XY:

1665

AN XY:

138656

show subpopulations

African (AFR)

AF:

0.00159

AC:

AN:

8830

American (AMR)

AF:

0.00119

AC:

AN:

10082

Ashkenazi Jewish (ASJ)

AF:

0.000203

AC:

AN:

9860

East Asian (EAS)

AF:

0.123

AC:

3064

AN:

24878

South Asian (SAS)

AF:

0.00689

AC:

AN:

5950

European-Finnish (FIN)

AF:

0.00

AC:

AN:

21578

Middle Eastern (MID)

AF:

0.0116

AC:

AN:

1378

European-Non Finnish (NFE)

AF:

0.000759

AC:

131

AN:

172638

Other (OTH)

AF:

0.00637

AC:

112

AN:

17592

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

146

291

437

582

728

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

102

136

170

<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:

0.00429

AC:

652

AN:

152040

Hom.:

Cov.:

AF XY:

0.00464

AC XY:

345

AN XY:

74292

show subpopulations

African (AFR)

AF:

0.00111

AC:

AN:

41528

American (AMR)

AF:

0.00105

AC:

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3470

East Asian (EAS)

AF:

0.0985

AC:

501

AN:

5086

South Asian (SAS)

AF:

0.00725

AC:

AN:

4826

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10586

Middle Eastern (MID)

AF:

0.0102

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.000648

AC:

AN:

67940

Other (OTH)

AF:

0.00331

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.511

Heterozygous variant carriers

127

159

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

100

<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:

0.00149

Hom.:

Bravo

AF:

0.00457

Asia WGS

AF:

0.0470

AC:

164

AN:

3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.68

CADD

Benign

(source)

DANN

Benign

0.92

PhyloP100

0.58

PromoterAI

0.034

Neutral

(source)

Mutation Taster

=300/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over