rs10513514

Variant names:

• chr3-157394168-T-C
• rs10513514
• NM_001167912.2:c.907-12792A>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.907-12792A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0672 in 152,296 control chromosomes in the GnomAD database, including 505 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 0.067 (505 hom., cov: 32)
• Consequence: VEPH1 NM_001167912.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.554
• Publications: 2 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:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.174 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
VEPH1	NM_001167912.2	c.907-12792A>G		intron_variant	Intron 6 of 13	ENST00000362010.7	NP_001161384.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
VEPH1	ENST00000362010.7	c.907-12792A>G		intron_variant	Intron 6 of 13	1	NM_001167912.2	ENSP00000354919.2
VEPH1	ENST00000392833.6	c.907-12792A>G		intron_variant	Intron 6 of 12	1		ENSP00000376578.2
VEPH1	ENST00000392832.6	c.907-12792A>G		intron_variant	Intron 6 of 13	2		ENSP00000376577.2
VEPH1	ENST00000482685.5	n.449-12792A>G		intron_variant	Intron 3 of 3	4

Frequencies

GnomAD3 genomes AF: 0.0671 AC: 10218 AN: 152178 Hom.: 504 Cov.: 32

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.0670

Gnomad AMR AF: 0.0313

Gnomad ASJ AF: 0.0991

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.0624

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0345

Gnomad OTH AF: 0.0554

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

GnomAD4 genome AF: 0.0672 AC: 10239 AN: 152296 Hom.: 505 Cov.: 32 AF XY: 0.0698 AC XY: 5198 AN XY: 74472

African (AFR) AF: 0.109 AC: 4527 AN: 41546

American (AMR) AF: 0.0312 AC: 478 AN: 15310

Ashkenazi Jewish (ASJ) AF: 0.0991 AC: 344 AN: 3470

East Asian (EAS) AF: 0.153 AC: 793 AN: 5186

South Asian (SAS) AF: 0.184 AC: 890 AN: 4824

European-Finnish (FIN) AF: 0.0624 AC: 662 AN: 10612

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0345 AC: 2346 AN: 68028

Other (OTH) AF: 0.0553 AC: 117 AN: 2116

Alfa AF: 0.0560 Hom.: 59

Bravo AF: 0.0640

Asia WGS AF: 0.171 AC: 595 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	0.47
DANN	Benign	0.53
PhyloP100		-0.55
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: rs10513514; hg19: chr3-157111957;