rs2137920

Variant names:

• chr10-49021593-T-A
• rs2137920
• NM_001031746.5:c.838-1818A>T

Your query was ambiguous. Multiple possible variants found:

• chr10-49021593-T-A
• chr10-49021593-T-C

Variant summary

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

The NM_001031746.5(VSTM4):​c.838-1818A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.677 in 151,958 control chromosomes in the GnomAD database, including 36,601 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 0.68 (36601 hom., cov: 31)
• Consequence: VSTM4 NM_001031746.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.11
• Publications: 5 publications found

Genes affected

VSTM4 (HGNC:26470): (V-set and transmembrane domain containing 4) Predicted to act upstream of or within several processes, including endothelial cell migration; retina blood vessel maintenance; and vasculature development. Predicted to be located in extracellular region and plasma membrane. Predicted to be integral component of 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.796 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
VSTM4	NM_001031746.5	c.838-1818A>T		intron_variant	Intron 7 of 7	ENST00000332853.9	NP_001026916.2
VSTM4	XM_017015827.3	c.998-1818A>T		intron_variant	Intron 8 of 8		XP_016871316.1
VSTM4	XM_047424711.1	c.983-1818A>T		intron_variant	Intron 8 of 8		XP_047280667.1
VSTM4	XR_001747052.3	n.875-1818A>T		intron_variant	Intron 7 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
VSTM4	ENST00000332853.9	c.838-1818A>T		intron_variant	Intron 7 of 7	1	NM_001031746.5	ENSP00000331062.3

Frequencies

GnomAD3 genomes AF: 0.677 AC: 102789 AN: 151842 Hom.: 36598 Cov.: 31

Gnomad AFR AF: 0.448

Gnomad AMI AF: 0.804

Gnomad AMR AF: 0.668

Gnomad ASJ AF: 0.724

Gnomad EAS AF: 0.679

Gnomad SAS AF: 0.502

Gnomad FIN AF: 0.823

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.802

Gnomad OTH AF: 0.702

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

GnomAD4 genome AF: 0.677 AC: 102824 AN: 151958 Hom.: 36601 Cov.: 31 AF XY: 0.672 AC XY: 49959 AN XY: 74298

African (AFR) AF: 0.448 AC: 18519 AN: 41328

American (AMR) AF: 0.669 AC: 10219 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.724 AC: 2512 AN: 3468

East Asian (EAS) AF: 0.679 AC: 3517 AN: 5180

South Asian (SAS) AF: 0.502 AC: 2415 AN: 4806

European-Finnish (FIN) AF: 0.823 AC: 8710 AN: 10582

Middle Eastern (MID) AF: 0.711 AC: 209 AN: 294

European-Non Finnish (NFE) AF: 0.802 AC: 54525 AN: 67998

Other (OTH) AF: 0.695 AC: 1466 AN: 2108

Alfa AF: 0.739 Hom.: 5326

Bravo AF: 0.662

Asia WGS AF: 0.548 AC: 1909 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.089
DANN	Benign	0.53
PhyloP100		-2.1
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: rs2137920; hg19: chr10-50229638;