Genetic Variant ENST00000812819.1:n.375+11516C>T (chr11-103668718-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 ENST00000812819.1(PDGFDDN):n.375+11516C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.731 in 152,104 control chromosomes in the GnomAD database, including 41,475 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 0.73 ( 41475 hom., cov: 32)

Consequence

PDGFDDN
ENST00000812819.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.106

Publications

2 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=-0.91).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.803 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.375+11516C>T		intron_variant	Intron 2 of 2
PDGFDDN	ENST00000812820.1 link	n.257+11516C>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.731

AC:

111053

AN:

151986

Hom.:

41432

Cov.:

show subpopulations

Gnomad AFR

AF:

0.599

Gnomad AMI

AF:

0.766

Gnomad AMR

AF:

0.715

Gnomad ASJ

AF:

0.728

Gnomad EAS

AF:

0.609

Gnomad SAS

AF:

0.661

Gnomad FIN

AF:

0.861

Gnomad MID

AF:

0.715

Gnomad NFE

AF:

0.809

Gnomad OTH

AF:

0.706

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

GnomAD4 genome

AF:

0.731

AC:

111151

AN:

152104

Hom.:

41475

Cov.:

AF XY:

0.729

AC XY:

54161

AN XY:

74332

show subpopulations

African (AFR)

AF:

0.599

AC:

24856

AN:

41482

American (AMR)

AF:

0.716

AC:

10926

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.728

AC:

2527

AN:

3470

East Asian (EAS)

AF:

0.609

AC:

3139

AN:

5154

South Asian (SAS)

AF:

0.659

AC:

3180

AN:

4822

European-Finnish (FIN)

AF:

0.861

AC:

9111

AN:

10584

Middle Eastern (MID)

AF:

0.724

AC:

213

AN:

294

European-Non Finnish (NFE)

AF:

0.809

AC:

55006

AN:

68010

Other (OTH)

AF:

0.708

AC:

1496

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1475

2950

4425

5900

7375

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

842

1684

2526

3368

4210

<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:

0.774

Hom.:

5988

Bravo

AF:

0.715

Asia WGS

AF:

0.657

AC:

2289

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

2.1

(source)

DANN

Benign

0.69

PhyloP100

-0.11

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