rs17175928

Variant names:

• chr10-49089520-C-A
• rs17175928
• NM_001031746.5:c.458-3497G>T

Variant summary

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

The NM_001031746.5(VSTM4):​c.458-3497G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.096 in 152,216 control chromosomes in the GnomAD database, including 939 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 0.096 (939 hom., cov: 33)
• Consequence: VSTM4 NM_001031746.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.821
• Publications: 2 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.199 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001031746.5. 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
	VSTM4	NM_001031746.5	MANE Select	c.458-3497G>T		intron	N/A	NP_001026916.2	Q8IW00-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	VSTM4	ENST00000332853.9	TSL:1 MANE Select	c.458-3497G>T		intron	N/A	ENSP00000331062.3	Q8IW00-1
	VSTM4	ENST00000956395.1		c.458-3497G>T		intron	N/A	ENSP00000626454.1

Frequencies

GnomAD3 genomes AF: 0.0961 AC: 14614 AN: 152098 Hom.: 939 Cov.: 33

Gnomad AFR AF: 0.0757

Gnomad AMI AF: 0.133

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.100

Gnomad EAS AF: 0.209

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.0476

Gnomad MID AF: 0.0987

Gnomad NFE AF: 0.0769

Gnomad OTH AF: 0.0880

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

GnomAD4 genome AF: 0.0960 AC: 14618 AN: 152216 Hom.: 939 Cov.: 33 AF XY: 0.0994 AC XY: 7395 AN XY: 74416

African (AFR) AF: 0.0756 AC: 3142 AN: 41536

American (AMR) AF: 0.195 AC: 2974 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.100 AC: 347 AN: 3470

East Asian (EAS) AF: 0.210 AC: 1086 AN: 5180

South Asian (SAS) AF: 0.209 AC: 1008 AN: 4812

European-Finnish (FIN) AF: 0.0476 AC: 505 AN: 10606

Middle Eastern (MID) AF: 0.0890 AC: 26 AN: 292

European-Non Finnish (NFE) AF: 0.0769 AC: 5227 AN: 68006

Other (OTH) AF: 0.0861 AC: 182 AN: 2114

Alfa AF: 0.0965 Hom.: 164

Bravo AF: 0.103

Asia WGS AF: 0.209 AC: 724 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.92
DANN	Benign	0.58
PhyloP100		-0.82
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: rs17175928; hg19: chr10-50297565;