Variant chrX-108067004-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2

The ENST00000217957.10(VSIG1):c.282C>T(p.Asn94=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00592 in 1,209,370 control chromosomes in the GnomAD database, including 19 homozygotes. There are 2,224 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0047 ( 1 hom., 124 hem., cov: 22)

Exomes 𝑓: 0.0060 ( 18 hom. 2100 hem. )

Consequence

VSIG1
ENST00000217957.10 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -1.65

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 -17 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BP6

Variant X-108067004-C-T is Benign according to our data. Variant chrX-108067004-C-T is described in ClinVar as [Benign]. Clinvar id is 771228.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-1.65 with no splicing effect.

BS2

High Hemizygotes in GnomAd4 at 124 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
VSIG1	NM_182607.5 linkuse as main transcript	c.282C>T	p.Asn94=	synonymous_variant	3/7	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.282C>T	p.Asn94=	synonymous_variant	3/7	1	NM_182607.5	ENSP00000217957	P2	Q86XK7-1
VSIG1	ENST00000415430.7 linkuse as main transcript	c.390C>T	p.Asn130=	synonymous_variant	4/8	2		ENSP00000402219	A2	Q86XK7-2
VSIG1	ENST00000458383.1 linkuse as main transcript	c.390C>T	p.Asn130=	synonymous_variant	4/4	4		ENSP00000407102
VSIG1	ENST00000485533.1 linkuse as main transcript	n.118C>T		non_coding_transcript_exon_variant	2/4	5

Frequencies

GnomAD3 genomes

AF:

0.00466

AC:

520

AN:

111627

Hom.:

Cov.:

AF XY:

0.00366

AC XY:

124

AN XY:

33837

show subpopulations

Gnomad AFR

AF:

0.000912

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00181

Gnomad ASJ

AF:

0.00113

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000761

Gnomad FIN

AF:

0.00132

Gnomad MID

AF:

0.0167

Gnomad NFE

AF:

0.00828

Gnomad OTH

AF:

0.0107

GnomAD3 exomes

AF:

0.00412

AC:

754

AN:

183145

Hom.:

AF XY:

0.00411

AC XY:

278

AN XY:

67719

show subpopulations

Gnomad AFR exome

AF:

0.000304

Gnomad AMR exome

AF:

0.00172

Gnomad ASJ exome

AF:

0.000669

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00110

Gnomad FIN exome

AF:

0.00119

Gnomad NFE exome

AF:

0.00773

Gnomad OTH exome

AF:

0.00597

GnomAD4 exome

AF:

0.00605

AC:

6638

AN:

1097689

Hom.:

Cov.:

AF XY:

0.00578

AC XY:

2100

AN XY:

363159

show subpopulations

Gnomad4 AFR exome

AF:

0.00125

Gnomad4 AMR exome

AF:

0.00165

Gnomad4 ASJ exome

AF:

0.000619

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000979

Gnomad4 FIN exome

AF:

0.00155

Gnomad4 NFE exome

AF:

0.00727

Gnomad4 OTH exome

AF:

0.00512

GnomAD4 genome

AF:

0.00466

AC:

520

AN:

111681

Hom.:

Cov.:

AF XY:

0.00366

AC XY:

124

AN XY:

33901

show subpopulations

Gnomad4 AFR

AF:

0.000910

Gnomad4 AMR

AF:

0.00181

Gnomad4 ASJ

AF:

0.00113

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000764

Gnomad4 FIN

AF:

0.00132

Gnomad4 NFE

AF:

0.00828

Gnomad4 OTH

AF:

0.0105

Alfa

AF:

0.00691

Hom.:

Bravo

AF:

0.00454

EpiCase

AF:

0.0105

EpiControl

AF:

0.0103

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Apr 03, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

0.18

DANN

Benign

0.54

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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