rs2120243

Variant names:

• chr3-157429779-A-C
• rs2120243
• NM_001167912.2:c.530-1291T>G

Your query was ambiguous. Multiple possible variants found:

• chr3-157429779-A-C
• chr3-157429779-A-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.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
• 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]

ACMG classification

Our verdict: Benign. The variant received -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.

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.530-1291T>G		intron	N/A	NP_001161384.1	Q14D04-1
	VEPH1	NM_024621.2		c.530-1291T>G		intron	N/A	NP_078897.2	Q14D04-1
	VEPH1	NM_001167911.2		c.530-1291T>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.530-1291T>G		intron	N/A	ENSP00000354919.2	Q14D04-1
	VEPH1	ENST00000392833.6	TSL:1	c.530-1291T>G		intron	N/A	ENSP00000376578.2	Q14D04-2
	VEPH1	ENST00000392832.6	TSL:2	c.530-1291T>G		intron	N/A	ENSP00000376577.2	Q14D04-1

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

African (AFR) AF: 0.648 AC: 26860 AN: 41454

American (AMR) AF: 0.654 AC: 10003 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.555 AC: 1925 AN: 3470

East Asian (EAS) AF: 0.673 AC: 3484 AN: 5180

South Asian (SAS) AF: 0.634 AC: 3061 AN: 4826

European-Finnish (FIN) AF: 0.521 AC: 5507 AN: 10560

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.554 AC: 37656 AN: 67968

Other (OTH) AF: 0.575 AC: 1210 AN: 2106

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.7
DANN	Benign	0.38
PhyloP100		-0.78
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: rs2120243; hg19: chr3-157147568;