3-157332376-T-C

Position:

• chr3-157332376-T-C

Variant summary

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

The ENST00000362010.7(VEPH1):​c.1736-15175A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.462 in 151,964 control chromosomes in the GnomAD database, including 18,117 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 0.46 (18117 hom., cov: 32)
• Consequence: VEPH1 ENST00000362010.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.806

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]

LOC101928236 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.587 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
VEPH1	NM_001167912.2	c.1736-15175A>G		intron_variant		ENST00000362010.7	NP_001161384.1
LOC101928236	XR_007096141.1	n.6565T>C		non_coding_transcript_exon_variant	7/10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
VEPH1	ENST00000362010.7	c.1736-15175A>G		intron_variant		1	NM_001167912.2	ENSP00000354919	P1
VEPH1	ENST00000392833.6	c.1736-15175A>G		intron_variant		1		ENSP00000376578
	ENST00000487238.5	n.332-48738T>C		intron_variant, non_coding_transcript_variant		4
VEPH1	ENST00000392832.6	c.1736-15175A>G		intron_variant		2		ENSP00000376577	P1

Frequencies

GnomAD3 genomes AF: 0.463 AC: 70235 AN: 151844 Hom.: 18115 Cov.: 32

Gnomad AFR AF: 0.217

Gnomad AMI AF: 0.717

Gnomad AMR AF: 0.597

Gnomad ASJ AF: 0.561

Gnomad EAS AF: 0.559

Gnomad SAS AF: 0.514

Gnomad FIN AF: 0.494

Gnomad MID AF: 0.417

Gnomad NFE AF: 0.557

Gnomad OTH AF: 0.488

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

GnomAD4 genome AF: 0.462 AC: 70264 AN: 151964 Hom.: 18117 Cov.: 32 AF XY: 0.463 AC XY: 34397 AN XY: 74260

Gnomad4 AFR AF: 0.217

Gnomad4 AMR AF: 0.597

Gnomad4 ASJ AF: 0.561

Gnomad4 EAS AF: 0.558

Gnomad4 SAS AF: 0.513

Gnomad4 FIN AF: 0.494

Gnomad4 NFE AF: 0.557

Gnomad4 OTH AF: 0.491

Alfa AF: 0.528 Hom.: 10981

Bravo AF: 0.458

Asia WGS AF: 0.532 AC: 1849 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.23
DANN	Benign	0.48

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: rs1581413; hg19: chr3-157050165;