rs144418706

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate

The NM_182607.5(VSIG1):​c.438C>A​(p.Ser146Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000413 in 1,209,384 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 2 hemizygotes in GnomAD. 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 0.0000089 ( 0 hom., 1 hem., cov: 23)
Exomes 𝑓: 0.0000036 ( 0 hom. 1 hem. )

Consequence

VSIG1
NM_182607.5 missense

Scores

3
14

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0520
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.13916299).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
VSIG1NM_182607.5 linkc.438C>A p.Ser146Arg missense_variant Exon 4 of 7 ENST00000217957.10 NP_872413.1 Q86XK7-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
VSIG1ENST00000217957.10 linkc.438C>A p.Ser146Arg missense_variant Exon 4 of 7 1 NM_182607.5 ENSP00000217957.3 Q86XK7-1
VSIG1ENST00000415430.7 linkc.546C>A p.Ser182Arg missense_variant Exon 5 of 8 2 ENSP00000402219.3 Q86XK7-2
VSIG1ENST00000485533.1 linkn.274C>A non_coding_transcript_exon_variant Exon 3 of 4 5

Frequencies

GnomAD3 genomes
AF:
0.00000894
AC:
1
AN:
111867
Hom.:
0
Cov.:
23
AF XY:
0.0000294
AC XY:
1
AN XY:
34035
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0000950
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.0000109
AC:
2
AN:
183171
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
67669
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.0000365
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000122
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.00000364
AC:
4
AN:
1097517
Hom.:
0
Cov.:
29
AF XY:
0.00000276
AC XY:
1
AN XY:
362943
show subpopulations
Gnomad4 AFR exome
AF:
0.0000379
Gnomad4 AMR exome
AF:
0.0000284
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000238
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.00000894
AC:
1
AN:
111867
Hom.:
0
Cov.:
23
AF XY:
0.0000294
AC XY:
1
AN XY:
34035
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.0000950
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00
Bravo
AF:
0.00000756
ExAC
AF:
0.00000824
AC:
1
EpiCase
AF:
0.00
EpiControl
AF:
0.0000594

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.37
BayesDel_addAF
Benign
-0.32
T
BayesDel_noAF
Benign
-0.59
CADD
Benign
21
DANN
Uncertain
1.0
DEOGEN2
Benign
0.042
.;T
FATHMM_MKL
Benign
0.47
N
LIST_S2
Benign
0.69
T;T
M_CAP
Benign
0.0063
T
MetaRNN
Benign
0.14
T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
1.6
.;L
PrimateAI
Benign
0.41
T
PROVEAN
Benign
-2.3
N;N
REVEL
Benign
0.16
Sift
Benign
0.17
T;T
Sift4G
Uncertain
0.035
D;D
Polyphen
1.0
.;D
Vest4
0.18
MutPred
0.46
.;Gain of catalytic residue at S146 (P = 0.038);
MVP
0.26
MPC
0.36
ClinPred
0.37
T
GERP RS
1.2
Varity_R
0.25
gMVP
0.55

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

LitVar

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

Other links and lift over

dbSNP: rs144418706; hg19: chrX-107315932; API