dbSNP rs3845978: VEPH1:c.530-13417G>A (chr3-157441905-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 NM_001167912.2(VEPH1):c.530-13417G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0941 in 151,886 control chromosomes in the GnomAD database, including 1,108 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 0.094 ( 1108 hom., cov: 32)

Consequence

VEPH1
NM_001167912.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0180

Publications

15 publications found

Variant links:

Genes affected

VEPH1 (HGNC:25735): (ventricular zone expressed PH domain containing 1) Predicted to enable phosphatidylinositol-5-phosphate binding activity. Involved in negative regulation of SMAD protein signal transduction and negative regulation of transforming growth factor beta receptor signaling pathway. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

VEPH1 links:

PTX3 (HGNC:9692): (pentraxin 3) This gene encodes a member of the pentraxin protein family. The expression of this protein is induced by inflammatory cytokines in response to inflammatory stimuli in several mesenchymal and epithelial cell types, particularly endothelial cells and mononuclear phagocytes. The protein promotes fibrocyte differentiation and is involved in regulating inflammation and complement activation. It also plays a role in angiogenesis and tissue remodeling. The protein serves as a biomarker for several inflammatory conditions. [provided by RefSeq, Jun 2016]

PTX3 links:

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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=-0.86).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.213 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
VEPH1	NM_001167912.2 link	c.530-13417G>A		intron_variant	Intron 4 of 13	ENST00000362010.7	NP_001161384.1	Q14D04-1
PTX3	NM_002852.4 link	c.533-461C>T		intron_variant	Intron 2 of 2	ENST00000295927.4	NP_002843.2	P26022

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
VEPH1	ENST00000362010.7 link	c.530-13417G>A		intron_variant	Intron 4 of 13	1	NM_001167912.2	ENSP00000354919.2		Q14D04-1
PTX3	ENST00000295927.4 link	c.533-461C>T		intron_variant	Intron 2 of 2	1	NM_002852.4	ENSP00000295927.3		P26022

Frequencies

GnomAD3 genomes

AF:

0.0940

AC:

14271

AN:

151782

Hom.:

1107

Cov.:

show subpopulations

Gnomad AFR

AF:

0.194

Gnomad AMI

AF:

0.0154

Gnomad AMR

AF:

0.0500

Gnomad ASJ

AF:

0.0692

Gnomad EAS

AF:

0.158

Gnomad SAS

AF:

0.224

Gnomad FIN

AF:

0.0560

Gnomad MID

AF:

0.0475

Gnomad NFE

AF:

0.0379

Gnomad OTH

AF:

0.0752

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

GnomAD4 genome

AF:

0.0941

AC:

14292

AN:

151886

Hom.:

1108

Cov.:

AF XY:

0.0962

AC XY:

7137

AN XY:

74186

show subpopulations

African (AFR)

AF:

0.194

AC:

8050

AN:

41392

American (AMR)

AF:

0.0498

AC:

760

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.0692

AC:

240

AN:

3468

East Asian (EAS)

AF:

0.158

AC:

816

AN:

5174

South Asian (SAS)

AF:

0.224

AC:

1078

AN:

4810

European-Finnish (FIN)

AF:

0.0560

AC:

587

AN:

10490

Middle Eastern (MID)

AF:

0.0476

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0379

AC:

2574

AN:

67972

Other (OTH)

AF:

0.0754

AC:

159

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

607

1213

1820

2426

3033

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

160

320

480

640

800

<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:

0.0569

Hom.:

1904

Bravo

AF:

0.0951

Asia WGS

AF:

0.187

AC:

650

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

7.7

(source)

DANN

Benign

0.68

PhyloP100

-0.018

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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