dbSNP rs10895516: PDGFDDN:n.128-32344C>T (chr11-103737242-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.128-32344C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0272 in 152,166 control chromosomes in the GnomAD database, including 134 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 0.027 ( 134 hom., cov: 32)

Consequence

PDGFDDN
ENST00000533459.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.901

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 (EAS) allele frequency at 95% confidence interval = 0.159 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.128-32344C>T	intron_variant	Intron 2 of 4	4
PDGFDDN	ENST00000812819.1 link	n.267-56900C>T	intron_variant	Intron 1 of 2
PDGFDDN	ENST00000812820.1 link	n.149-56900C>T	intron_variant	Intron 1 of 3
PDGFDDN	ENST00000812821.1 link	n.154-56900C>T	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.0272

AC:

4139

AN:

152048

Hom.:

134

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0371

Gnomad AMI

AF:

0.00219

Gnomad AMR

AF:

0.0182

Gnomad ASJ

AF:

0.0130

Gnomad EAS

AF:

0.168

Gnomad SAS

AF:

0.0503

Gnomad FIN

AF:

0.00972

Gnomad MID

AF:

0.0475

Gnomad NFE

AF:

0.0146

Gnomad OTH

AF:

0.0249

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

GnomAD4 genome

AF:

0.0272

AC:

4140

AN:

152166

Hom.:

134

Cov.:

AF XY:

0.0280

AC XY:

2084

AN XY:

74360

show subpopulations

African (AFR)

AF:

0.0372

AC:

1544

AN:

41522

American (AMR)

AF:

0.0181

AC:

277

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.0130

AC:

AN:

3470

East Asian (EAS)

AF:

0.168

AC:

868

AN:

5162

South Asian (SAS)

AF:

0.0505

AC:

243

AN:

4810

European-Finnish (FIN)

AF:

0.00972

AC:

103

AN:

10594

Middle Eastern (MID)

AF:

0.0476

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0146

AC:

993

AN:

68018

Other (OTH)

AF:

0.0241

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

192

384

577

769

961

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

104

156

208

260

<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:

0.0182

Hom.:

Bravo

AF:

0.0280

Asia WGS

AF:

0.0960

AC:

331

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.68

(source)

DANN

Benign

0.50

PhyloP100

-0.90

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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