rs2120243

chr3-157429779-A-Cchr3-157429779-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001167912.2(VEPH1):c.530-1291T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.594 in 152,050 control chromosomes in the GnomAD database, including 27,096 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 0.59 (27096 hom., cov: 32)
• Consequence: VEPH1 NM_001167912.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.781

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.654 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
VEPH1	NM_001167912.2	c.530-1291T>G		intron_variant		ENST00000362010.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
VEPH1	ENST00000362010.7	c.530-1291T>G		intron_variant		1	NM_001167912.2	P1

Frequencies

GnomAD3 genomes AF: 0.594 AC: 90290 AN: 151932 Hom.: 27067 Cov.: 32

Gnomad AFR AF: 0.648

Gnomad AMI AF: 0.574

Gnomad AMR AF: 0.655

Gnomad ASJ AF: 0.555

Gnomad EAS AF: 0.673

Gnomad SAS AF: 0.635

Gnomad FIN AF: 0.521

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.554

Gnomad OTH AF: 0.569

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

GnomAD4 genome AF: 0.594 AC: 90381 AN: 152050 Hom.: 27096 Cov.: 32 AF XY: 0.596 AC XY: 44258 AN XY: 74304

Gnomad4 AFR AF: 0.648

Gnomad4 AMR AF: 0.654

Gnomad4 ASJ AF: 0.555

Gnomad4 EAS AF: 0.673

Gnomad4 SAS AF: 0.634

Gnomad4 FIN AF: 0.521

Gnomad4 NFE AF: 0.554

Gnomad4 OTH AF: 0.575

Alfa AF: 0.514 Hom.: 2296

Bravo AF: 0.604

Asia WGS AF: 0.691 AC: 2402 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	1.7
Dann	Benign	0.38

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

LitVar

Other links and lift over

dbSNP: rs2120243; hg19: chr3-157147568;