19-54050443-T-C

Variant names:

• chr19-54050443-T-C
• rs10500316
• NM_198481.4:c.394+967A>G

Variant summary

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

The NM_198481.4(VSTM1):​c.394+967A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.516 in 151,782 control chromosomes in the GnomAD database, including 20,526 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 0.52 (20526 hom., cov: 30)
• Consequence: VSTM1 NM_198481.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0510
• Publications: 18 publications found

Genes affected

VSTM1 (HGNC:29455): (V-set and transmembrane domain containing 1) Predicted to enable cytokine activity. Predicted to be involved in immune system process and signal transduction. Predicted to be located in extracellular space. 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=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.538 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
VSTM1	NM_198481.4	c.394+967A>G		intron_variant	Intron 4 of 8	ENST00000338372.7	NP_940883.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
VSTM1	ENST00000338372.7	c.394+967A>G		intron_variant	Intron 4 of 8	1	NM_198481.4	ENSP00000343366.2

Frequencies

GnomAD3 genomes AF: 0.516 AC: 78224 AN: 151664 Hom.: 20490 Cov.: 30

Gnomad AFR AF: 0.514

Gnomad AMI AF: 0.659

Gnomad AMR AF: 0.528

Gnomad ASJ AF: 0.581

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.382

Gnomad FIN AF: 0.522

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.543

Gnomad OTH AF: 0.498

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

GnomAD4 genome AF: 0.516 AC: 78326 AN: 151782 Hom.: 20526 Cov.: 30 AF XY: 0.511 AC XY: 37887 AN XY: 74138

African (AFR) AF: 0.515 AC: 21298 AN: 41388

American (AMR) AF: 0.529 AC: 8047 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.581 AC: 2009 AN: 3458

East Asian (EAS) AF: 0.186 AC: 962 AN: 5178

South Asian (SAS) AF: 0.383 AC: 1842 AN: 4808

European-Finnish (FIN) AF: 0.522 AC: 5482 AN: 10506

Middle Eastern (MID) AF: 0.531 AC: 155 AN: 292

European-Non Finnish (NFE) AF: 0.543 AC: 36880 AN: 67912

Other (OTH) AF: 0.498 AC: 1050 AN: 2108

Alfa AF: 0.525 Hom.: 55724

Bravo AF: 0.518

Asia WGS AF: 0.314 AC: 1091 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.0
DANN	Benign	0.30
PhyloP100		0.051
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: rs10500316; hg19: chr19-54553697;