Genetic Variant PDGFDDN:n.128-31112C>T (chr11-103736010-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 ENST00000533459.1(PDGFDDN):n.128-31112C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0523 in 152,260 control chromosomes in the GnomAD database, including 423 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 0.052 ( 423 hom., cov: 32)

Consequence

PDGFDDN
ENST00000533459.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.301

Publications

1 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=-0.89).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.16 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
PDGFDDN	ENST00000533459.1 link	n.128-31112C>T	intron_variant	Intron 2 of 4	4
PDGFDDN	ENST00000812819.1 link	n.267-55668C>T	intron_variant	Intron 1 of 2
PDGFDDN	ENST00000812820.1 link	n.149-55668C>T	intron_variant	Intron 1 of 3
PDGFDDN	ENST00000812821.1 link	n.154-55668C>T	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.0523

AC:

7956

AN:

152144

Hom.:

419

Cov.:

show subpopulations

Gnomad AFR

AF:

0.123

Gnomad AMI

AF:

0.00219

Gnomad AMR

AF:

0.0315

Gnomad ASJ

AF:

0.0130

Gnomad EAS

AF:

0.169

Gnomad SAS

AF:

0.0515

Gnomad FIN

AF:

0.00998

Gnomad MID

AF:

0.0538

Gnomad NFE

AF:

0.0149

Gnomad OTH

AF:

0.0435

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

GnomAD4 genome

AF:

0.0523

AC:

7970

AN:

152260

Hom.:

423

Cov.:

AF XY:

0.0521

AC XY:

3881

AN XY:

74438

show subpopulations

African (AFR)

AF:

0.123

AC:

5092

AN:

41524

American (AMR)

AF:

0.0314

AC:

480

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.0130

AC:

AN:

3470

East Asian (EAS)

AF:

0.169

AC:

872

AN:

5166

South Asian (SAS)

AF:

0.0518

AC:

250

AN:

4830

European-Finnish (FIN)

AF:

0.00998

AC:

106

AN:

10622

Middle Eastern (MID)

AF:

0.0548

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.0149

AC:

1017

AN:

68032

Other (OTH)

AF:

0.0425

AC:

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

376

753

1129

1506

1882

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

180

270

360

450

<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:

0.0265

Hom.:

223

Bravo

AF:

0.0576

Asia WGS

AF:

0.101

AC:

349

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.97

(source)

DANN

Benign

0.74

PhyloP100

-0.30

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