Genetic Variant VSTM4:c.*2929G>A (chr10-49016721-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001031746.5(VSTM4):c.*2929G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.676 in 152,208 control chromosomes in the GnomAD database, including 36,614 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 ( 36613 hom., cov: 34)

Exomes 𝑓: 0.75 ( 1 hom. )

Consequence

VSTM4
NM_001031746.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.122

Publications

12 publications found

Variant links:

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]

VSTM4 links:

ENSG00000226576 (HGNC:):

ENSG00000226576 links:

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ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.796 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
VSTM4	NM_001031746.5 link	c.*2929G>A	3_prime_UTR_variant	Exon 8 of 8	ENST00000332853.9	NP_001026916.2	Q8IW00-1
VSTM4	XR_001747052.3 link	n.3370G>A	non_coding_transcript_exon_variant	Exon 9 of 9
VSTM4	XM_017015827.3 link	c.*3041G>A	3_prime_UTR_variant	Exon 9 of 9		XP_016871316.1
VSTM4	XM_047424711.1 link	c.*3041G>A	3_prime_UTR_variant	Exon 9 of 9		XP_047280667.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
VSTM4	ENST00000332853.9 link	c.*2929G>A		3_prime_UTR_variant	Exon 8 of 8	1	NM_001031746.5	ENSP00000331062.3		Q8IW00-1
ENSG00000226576	ENST00000422966.1 link	n.403-2105C>T		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes

AF:

0.676

AC:

102845

AN:

152086

Hom.:

36610

Cov.:

show subpopulations

Gnomad AFR

AF:

0.447

Gnomad AMI

AF:

0.804

Gnomad AMR

AF:

0.668

Gnomad ASJ

AF:

0.724

Gnomad EAS

AF:

0.678

Gnomad SAS

AF:

0.502

Gnomad FIN

AF:

0.823

Gnomad MID

AF:

0.703

Gnomad NFE

AF:

0.802

Gnomad OTH

AF:

0.701

GnomAD4 exome

AF:

0.750

AC:

AN:

Hom.:

Cov.:

AF XY:

0.500

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.750

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.525

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.676

AC:

102880

AN:

152204

Hom.:

36613

Cov.:

AF XY:

0.672

AC XY:

49974

AN XY:

74406

show subpopulations

African (AFR)

AF:

0.447

AC:

18559

AN:

41512

American (AMR)

AF:

0.669

AC:

10226

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.724

AC:

2514

AN:

3472

East Asian (EAS)

AF:

0.678

AC:

3506

AN:

5170

South Asian (SAS)

AF:

0.501

AC:

2417

AN:

4820

European-Finnish (FIN)

AF:

0.823

AC:

8730

AN:

10608

Middle Eastern (MID)

AF:

0.711

AC:

209

AN:

294

European-Non Finnish (NFE)

AF:

0.802

AC:

54523

AN:

68014

Other (OTH)

AF:

0.694

AC:

1463

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

1565

3129

4694

6258

7823

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.747

Hom.:

78906

Bravo

AF:

0.661

Asia WGS

AF:

0.548

AC:

1910

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

6.0

(source)

DANN

Benign

0.51

PhyloP100

-0.12

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

Publications

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10-49016721-C-T

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over