Genetic Variant PDGFDDN:n.376-20479G>A (chr11-103659564-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 ENST00000812819.1(PDGFDDN):n.376-20479G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.235 in 152,060 control chromosomes in the GnomAD database, including 4,538 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 0.24 ( 4538 hom., cov: 32)

Consequence

PDGFDDN
ENST00000812819.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.22

Publications

3 publications found

Variant links:

Genes affected

PDGFDDN (HGNC:56909):

PDGFDDN 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 = 0.31 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PDGFDDN	ENST00000812819.1 link	n.376-20479G>A		intron_variant	Intron 2 of 2
PDGFDDN	ENST00000812820.1 link	n.258-8469G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.235

AC:

35733

AN:

151942

Hom.:

4512

Cov.:

show subpopulations

Gnomad AFR

AF:

0.313

Gnomad AMI

AF:

0.188

Gnomad AMR

AF:

0.182

Gnomad ASJ

AF:

0.188

Gnomad EAS

AF:

0.122

Gnomad SAS

AF:

0.190

Gnomad FIN

AF:

0.227

Gnomad MID

AF:

0.203

Gnomad NFE

AF:

0.216

Gnomad OTH

AF:

0.223

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

GnomAD4 genome

AF:

0.235

AC:

35802

AN:

152060

Hom.:

4538

Cov.:

AF XY:

0.233

AC XY:

17290

AN XY:

74328

show subpopulations

African (AFR)

AF:

0.314

AC:

13021

AN:

41458

American (AMR)

AF:

0.182

AC:

2774

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.188

AC:

652

AN:

3472

East Asian (EAS)

AF:

0.122

AC:

630

AN:

5176

South Asian (SAS)

AF:

0.191

AC:

920

AN:

4816

European-Finnish (FIN)

AF:

0.227

AC:

2401

AN:

10572

Middle Eastern (MID)

AF:

0.214

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.216

AC:

14705

AN:

67980

Other (OTH)

AF:

0.221

AC:

465

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1361

2722

4082

5443

6804

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

374

748

1122

1496

1870

<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:

0.198

Hom.:

2197

Bravo

AF:

0.238

Asia WGS

AF:

0.150

AC:

525

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.036

(source)

DANN

Benign

0.33

PhyloP100

-2.2

Splicing

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over