3-157332376-T-C

Variant names:

• chr3-157332376-T-C
• rs1581413
• NM_001167912.2:c.1736-15175A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001167912.2(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 NM_001167912.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.806
• Publications: 15 publications found

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:):

LINC00881 (HGNC:48567): (long intergenic non-protein coding RNA 881)

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001167912.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	VEPH1	NM_001167912.2	MANE Select	c.1736-15175A>G		intron	N/A	NP_001161384.1	Q14D04-1
	VEPH1	NM_024621.2		c.1736-15175A>G		intron	N/A	NP_078897.2	Q14D04-1
	VEPH1	NM_001167911.2		c.1736-15175A>G		intron	N/A	NP_001161383.1	Q14D04-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	VEPH1	ENST00000362010.7	TSL:1 MANE Select	c.1736-15175A>G		intron	N/A	ENSP00000354919.2	Q14D04-1
	VEPH1	ENST00000392833.6	TSL:1	c.1736-15175A>G		intron	N/A	ENSP00000376578.2	Q14D04-2
	VEPH1	ENST00000392832.6	TSL:2	c.1736-15175A>G		intron	N/A	ENSP00000376577.2	Q14D04-1

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

African (AFR) AF: 0.217 AC: 8985 AN: 41428

American (AMR) AF: 0.597 AC: 9122 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.561 AC: 1947 AN: 3470

East Asian (EAS) AF: 0.558 AC: 2882 AN: 5166

South Asian (SAS) AF: 0.513 AC: 2474 AN: 4818

European-Finnish (FIN) AF: 0.494 AC: 5214 AN: 10546

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.557 AC: 37827 AN: 67950

Other (OTH) AF: 0.491 AC: 1036 AN: 2108

Alfa AF: 0.527 Hom.: 12142

Bravo AF: 0.458

Asia WGS AF: 0.532 AC: 1849 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.23
DANN	Benign	0.48
PhyloP100		-0.81
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1581413; hg19: chr3-157050165;