Genetic Variant ENST00000533459.1:n.128-84941A>G (chr11-103789839-T-C) – 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.128-84941A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.642 in 152,068 control chromosomes in the GnomAD database, including 32,345 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 0.64 ( 32345 hom., cov: 32)

Consequence

PDGFDDN
ENST00000533459.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.435

Publications

103 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=-0.84).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.722 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.128-84941A>G	intron_variant	Intron 2 of 4	4
PDGFDDN	ENST00000812819.1 link	n.266+13149A>G	intron_variant	Intron 1 of 2
PDGFDDN	ENST00000812820.1 link	n.148+13149A>G	intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.642

AC:

97572

AN:

151950

Hom.:

32322

Cov.:

show subpopulations

Gnomad AFR

AF:

0.503

Gnomad AMI

AF:

0.681

Gnomad AMR

AF:

0.733

Gnomad ASJ

AF:

0.624

Gnomad EAS

AF:

0.392

Gnomad SAS

AF:

0.644

Gnomad FIN

AF:

0.778

Gnomad MID

AF:

0.589

Gnomad NFE

AF:

0.705

Gnomad OTH

AF:

0.634

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

GnomAD4 genome

AF:

0.642

AC:

97636

AN:

152068

Hom.:

32345

Cov.:

AF XY:

0.644

AC XY:

47837

AN XY:

74338

show subpopulations

African (AFR)

AF:

0.503

AC:

20867

AN:

41466

American (AMR)

AF:

0.733

AC:

11198

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.624

AC:

2167

AN:

3470

East Asian (EAS)

AF:

0.392

AC:

2025

AN:

5170

South Asian (SAS)

AF:

0.643

AC:

3101

AN:

4820

European-Finnish (FIN)

AF:

0.778

AC:

8230

AN:

10574

Middle Eastern (MID)

AF:

0.585

AC:

172

AN:

294

European-Non Finnish (NFE)

AF:

0.705

AC:

47915

AN:

67982

Other (OTH)

AF:

0.635

AC:

1340

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1701

3402

5103

6804

8505

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

792

1584

2376

3168

3960

<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:

0.681

Hom.:

150286

Bravo

AF:

0.634

Asia WGS

AF:

0.575

AC:

2002

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

5.3

(source)

DANN

Benign

0.74

PhyloP100

0.43

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