chr3-157428216-G-A

Variant names:

• chr3-157428216-G-A
• rs9289983
• NM_001167912.2:c.696+106C>T

Variant summary

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

The NM_001167912.2(VEPH1):​c.696+106C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.488 in 1,205,104 control chromosomes in the GnomAD database, including 147,854 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 0.41 (14659 hom., cov: 33)
  • Exomes 𝑓: 0.50 (133195 hom.)
• Consequence: VEPH1 NM_001167912.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.541
• Publications: 4 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.558 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
VEPH1	NM_001167912.2	c.696+106C>T		intron_variant	Intron 5 of 13	ENST00000362010.7	NP_001161384.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
VEPH1	ENST00000362010.7	c.696+106C>T		intron_variant	Intron 5 of 13	1	NM_001167912.2	ENSP00000354919.2

Frequencies

GnomAD3 genomes AF: 0.413 AC: 62733 AN: 151976 Hom.: 14655 Cov.: 33

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.553

Gnomad AMR AF: 0.567

Gnomad ASJ AF: 0.478

Gnomad EAS AF: 0.480

Gnomad SAS AF: 0.372

Gnomad FIN AF: 0.467

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.505

Gnomad OTH AF: 0.430

GnomAD4 exome AF: 0.499 AC: 524965 AN: 1053010 Hom.: 133195 AF XY: 0.498 AC XY: 259100 AN XY: 520174

African (AFR) AF: 0.168 AC: 3823 AN: 22750

American (AMR) AF: 0.626 AC: 15394 AN: 24572

Ashkenazi Jewish (ASJ) AF: 0.492 AC: 8219 AN: 16718

East Asian (EAS) AF: 0.488 AC: 17071 AN: 34954

South Asian (SAS) AF: 0.410 AC: 18067 AN: 44016

European-Finnish (FIN) AF: 0.485 AC: 21607 AN: 44512

Middle Eastern (MID) AF: 0.426 AC: 1347 AN: 3162

European-Non Finnish (NFE) AF: 0.512 AC: 418360 AN: 817740

Other (OTH) AF: 0.473 AC: 21077 AN: 44586

GnomAD4 genome AF: 0.413 AC: 62751 AN: 152094 Hom.: 14659 Cov.: 33 AF XY: 0.414 AC XY: 30765 AN XY: 74310

African (AFR) AF: 0.177 AC: 7341 AN: 41516

American (AMR) AF: 0.568 AC: 8672 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.478 AC: 1658 AN: 3468

East Asian (EAS) AF: 0.480 AC: 2473 AN: 5152

South Asian (SAS) AF: 0.372 AC: 1789 AN: 4814

European-Finnish (FIN) AF: 0.467 AC: 4932 AN: 10562

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.505 AC: 34335 AN: 67986

Other (OTH) AF: 0.434 AC: 917 AN: 2112

Alfa AF: 0.468 Hom.: 12058

Bravo AF: 0.411

Asia WGS AF: 0.436 AC: 1515 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.59
DANN	Benign	0.55
PhyloP100		-0.54
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs9289983; hg19: chr3-157146005;