Variant X-108061477-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2

The ENST00000217957.10(VSIG1):c.213+3276A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00258 in 1,165,387 control chromosomes in the GnomAD database, including 7 homozygotes. There are 969 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0018 ( 0 hom., 61 hem., cov: 22)

Exomes 𝑓: 0.0027 ( 7 hom. 908 hem. )

Consequence

VSIG1
ENST00000217957.10 intron

Scores

Clinical Significance

Likely benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 1.55

Variant links:

Genes affected

VSIG1 (HGNC:28675): (V-set and immunoglobulin domain containing 1) This gene encodes a member of the junctional adhesion molecule (JAM) family. The encoded protein contains multiple glycosylation sites at the N-terminal region, and multiple phosphorylation sites and glutamic acid/proline (EP) repeats at the C-terminal region. The gene is expressed in normal stomach and testis, as well as in gastric, esophageal and ovarian cancers. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2009]

VSIG1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.013447851).

BP6

Variant X-108061477-A-G is Benign according to our data. Variant chrX-108061477-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 718703.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS2

High Hemizygotes in GnomAd4 at 61 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
VSIG1	NM_182607.5 linkuse as main transcript	c.213+3276A>G		intron_variant		ENST00000217957.10	NP_872413.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
VSIG1	ENST00000217957.10 linkuse as main transcript	c.213+3276A>G		intron_variant		1	NM_182607.5	ENSP00000217957	P2	Q86XK7-1
VSIG1	ENST00000415430.7 linkuse as main transcript	c.263A>G	p.Gln88Arg	missense_variant	3/8	2		ENSP00000402219	A2	Q86XK7-2
VSIG1	ENST00000458383.1 linkuse as main transcript	c.263A>G	p.Gln88Arg	missense_variant	3/4	4		ENSP00000407102

Frequencies

GnomAD3 genomes

AF:

0.00183

AC:

204

AN:

111463

Hom.:

Cov.:

AF XY:

0.00181

AC XY:

AN XY:

33661

show subpopulations

Gnomad AFR

AF:

0.000196

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0000949

Gnomad ASJ

AF:

0.00151

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000381

Gnomad FIN

AF:

0.000656

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00351

Gnomad OTH

AF:

0.00134

GnomAD3 exomes

AF:

0.00125

AC:

143

AN:

114143

Hom.:

AF XY:

0.00115

AC XY:

AN XY:

40849

show subpopulations

Gnomad AFR exome

AF:

0.000301

Gnomad AMR exome

AF:

0.000308

Gnomad ASJ exome

AF:

0.000799

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.000544

Gnomad NFE exome

AF:

0.00271

Gnomad OTH exome

AF:

0.00181

GnomAD4 exome

AF:

0.00266

AC:

2805

AN:

1053869

Hom.:

Cov.:

AF XY:

0.00263

AC XY:

908

AN XY:

344807

show subpopulations

Gnomad4 AFR exome

AF:

0.000201

Gnomad4 AMR exome

AF:

0.000394

Gnomad4 ASJ exome

AF:

0.000859

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.000795

Gnomad4 NFE exome

AF:

0.00323

Gnomad4 OTH exome

AF:

0.00214

GnomAD4 genome

AF:

0.00183

AC:

204

AN:

111518

Hom.:

Cov.:

AF XY:

0.00181

AC XY:

AN XY:

33726

show subpopulations

Gnomad4 AFR

AF:

0.000196

Gnomad4 AMR

AF:

0.0000948

Gnomad4 ASJ

AF:

0.00151

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000382

Gnomad4 FIN

AF:

0.000656

Gnomad4 NFE

AF:

0.00351

Gnomad4 OTH

AF:

0.00132

Alfa

AF:

0.00254

Hom.:

108

Bravo

AF:

0.00148

TwinsUK

AF:

0.00270

AC:

ALSPAC

AF:

0.00208

AC:

ESP6500AA

AF:

0.00

AC:

ESP6500EA

AF:

0.00293

AC:

ExAC

AF:

0.00114

AC:

ClinVar

Significance: Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Likely benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Likely benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Nov 30, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.12

BayesDel_noAF

Uncertain

0.050

CADD

Benign

DANN

Uncertain

1.0

DEOGEN2

Benign

0.020

.;T

FATHMM_MKL

Uncertain

0.76

LIST_S2

Benign

0.42

T;T

M_CAP

Pathogenic

0.56

MetaRNN

Benign

0.013

T;T

MetaSVM

Uncertain

0.51

MutationTaster

Benign

1.0

D;N

PrimateAI

Benign

0.38

PROVEAN

Benign

-0.69

N;N

REVEL

Uncertain

0.43

Sift

Uncertain

0.0050

D;T

Sift4G

Pathogenic

0.0

D;D

Vest4

0.29

MVP

0.46

MPC

0.49

ClinPred

0.034

GERP RS

4.8

gMVP

0.74

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.14

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over