Variant 4-156970791-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_016205.3(PDGFC):c.113A>G(p.Gln38Arg) variant causes a missense change. The variant allele was found at a frequency of 0.00546 in 1,588,684 control chromosomes in the GnomAD database, including 40 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0045 ( 0 hom., cov: 32)

Exomes 𝑓: 0.0056 ( 40 hom. )

Consequence

PDGFC
NM_016205.3 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 3.81

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 made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.005934298).

BP6

Variant 4-156970791-T-C is Benign according to our data. Variant chr4-156970791-T-C is described in ClinVar as [Benign]. Clinvar id is 771707.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High AC in GnomAd4 at 691 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PDGFC	NM_016205.3 linkuse as main transcript	c.113A>G	p.Gln38Arg	missense_variant	1/6	ENST00000502773.6
PDGFC	NR_036641.2 linkuse as main transcript	n.1009A>G		non_coding_transcript_exon_variant	1/7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PDGFC	ENST00000502773.6 linkuse as main transcript	c.113A>G	p.Gln38Arg	missense_variant	1/6	1	NM_016205.3	P1	Q9NRA1-1
PDGFC	ENST00000274071.6 linkuse as main transcript	c.113A>G	p.Gln38Arg	missense_variant, NMD_transcript_variant	1/7	1
PDGFC	ENST00000422544.2 linkuse as main transcript	c.113A>G	p.Gln38Arg	missense_variant	1/6	5			Q9NRA1-2
PDGFC	ENST00000513664.1 linkuse as main transcript	n.175A>G		non_coding_transcript_exon_variant	1/2	3

Frequencies

GnomAD3 genomes

AF:

0.00454

AC:

691

AN:

152224

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00118

Gnomad AMI

AF:

0.00658

Gnomad AMR

AF:

0.00360

Gnomad ASJ

AF:

0.000576

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000828

Gnomad FIN

AF:

0.00358

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.00764

Gnomad OTH

AF:

0.00669

GnomAD3 exomes

AF:

0.00443

AC:

1113

AN:

251412

Hom.:

AF XY:

0.00432

AC XY:

587

AN XY:

135886

show subpopulations

Gnomad AFR exome

AF:

0.00129

Gnomad AMR exome

AF:

0.00243

Gnomad ASJ exome

AF:

0.000496

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00105

Gnomad FIN exome

AF:

0.00379

Gnomad NFE exome

AF:

0.00759

Gnomad OTH exome

AF:

0.00424

GnomAD4 exome

AF:

0.00555

AC:

7977

AN:

1436342

Hom.:

Cov.:

AF XY:

0.00546

AC XY:

3907

AN XY:

716060

show subpopulations

Gnomad4 AFR exome

AF:

0.000910

Gnomad4 AMR exome

AF:

0.00213

Gnomad4 ASJ exome

AF:

0.000385

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000933

Gnomad4 FIN exome

AF:

0.00376

Gnomad4 NFE exome

AF:

0.00674

Gnomad4 OTH exome

AF:

0.00358

GnomAD4 genome

AF:

0.00454

AC:

691

AN:

152342

Hom.:

Cov.:

AF XY:

0.00447

AC XY:

333

AN XY:

74492

show subpopulations

Gnomad4 AFR

AF:

0.00118

Gnomad4 AMR

AF:

0.00359

Gnomad4 ASJ

AF:

0.000576

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000829

Gnomad4 FIN

AF:

0.00358

Gnomad4 NFE

AF:

0.00764

Gnomad4 OTH

AF:

0.00662

Alfa

AF:

0.00661

Hom.:

Bravo

AF:

0.00419

TwinsUK

AF:

0.00512

AC:

ALSPAC

AF:

0.00675

AC:

ESP6500AA

AF:

0.00159

AC:

ESP6500EA

AF:

0.00663

AC:

ExAC

AF:

0.00450

AC:

546

Asia WGS

AF:

0.000866

AC:

AN:

3478

EpiCase

AF:

0.00556

EpiControl

AF:

0.00634

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Dec 31, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.098

BayesDel_addAF

Benign

-0.50

BayesDel_noAF

Benign

-0.48

CADD

Benign

DANN

Benign

0.60

DEOGEN2

Benign

0.19

T;.

Eigen

Benign

-0.64

Eigen_PC

Benign

-0.57

FATHMM_MKL

Uncertain

0.87

LIST_S2

Benign

0.71

T;T

M_CAP

Benign

0.030

MetaRNN

Benign

0.0059

T;T

MetaSVM

Benign

-1.1

MutationAssessor

Benign

0.90

L;L

MutationTaster

Benign

0.94

D;D;D

PrimateAI

Benign

0.43

PROVEAN

Benign

-0.22

N;N

REVEL

Benign

0.088

Sift

Benign

0.36

T;T

Sift4G

Benign

0.28

T;T

Polyphen

0.046

B;.

Vest4

0.37

MVP

0.36

MPC

0.34

ClinPred

0.013

GERP RS

1.1

Varity_R

0.13

gMVP

0.47

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over