NM_182607.5:c.1061C>A

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2

The NM_182607.5(VSIG1):​c.1061C>A​(p.Thr354Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000967 in 1,210,321 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 27 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

Frequency

Genomes: 𝑓 0.00059 ( 0 hom., 15 hem., cov: 23)
Exomes 𝑓: 0.000046 ( 0 hom. 12 hem. )

Consequence

VSIG1
NM_182607.5 missense

Scores

1
15

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:1B:1

Conservation

PhyloP100: -2.21
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.0055253804).
BP6
Variant X-108077278-C-A is Benign according to our data. Variant chrX-108077278-C-A is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 738138.We mark this variant Likely_benign, oryginal submissions are: {Uncertain_significance=1, Likely_benign=1}.
BS2
High Hemizygotes in GnomAd4 at 15 gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
VSIG1NM_182607.5 linkc.1061C>A p.Thr354Lys missense_variant Exon 7 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.1061C>A p.Thr354Lys missense_variant Exon 7 of 7 1 NM_182607.5 ENSP00000217957.3 Q86XK7-1
VSIG1ENST00000415430.7 linkc.1169C>A p.Thr390Lys missense_variant Exon 8 of 8 2 ENSP00000402219.3 Q86XK7-2

Frequencies

GnomAD3 genomes
AF:
0.000580
AC:
65
AN:
112020
Hom.:
0
Cov.:
23
AF XY:
0.000439
AC XY:
15
AN XY:
34174
show subpopulations
Gnomad AFR
AF:
0.00205
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0000946
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:
0.000668
GnomAD3 exomes
AF:
0.000153
AC:
28
AN:
183309
Hom.:
0
AF XY:
0.0000885
AC XY:
6
AN XY:
67803
show subpopulations
Gnomad AFR exome
AF:
0.00198
Gnomad AMR exome
AF:
0.0000729
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:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000464
AC:
51
AN:
1098250
Hom.:
0
Cov.:
31
AF XY:
0.0000330
AC XY:
12
AN XY:
363610
show subpopulations
Gnomad4 AFR exome
AF:
0.00159
Gnomad4 AMR exome
AF:
0.0000852
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:
0.00
Gnomad4 OTH exome
AF:
0.000130
GnomAD4 genome
AF:
0.000589
AC:
66
AN:
112071
Hom.:
0
Cov.:
23
AF XY:
0.000438
AC XY:
15
AN XY:
34235
show subpopulations
Gnomad4 AFR
AF:
0.00208
Gnomad4 AMR
AF:
0.0000945
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:
0.000659
Alfa
AF:
0.0000383
Hom.:
2
Bravo
AF:
0.000597
ESP6500AA
AF:
0.00261
AC:
10
ESP6500EA
AF:
0.00
AC:
0
ExAC
AF:
0.000222
AC:
27

ClinVar

Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:1Benign:1
Revision: criteria provided, conflicting classifications
LINK: link

Submissions by phenotype

not specified Uncertain:1
Aug 19, 2024
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.1169C>A (p.T390K) alteration is located in exon 8 (coding exon 8) of the VSIG1 gene. This alteration results from a C to A substitution at nucleotide position 1169, causing the threonine (T) at amino acid position 390 to be replaced by a lysine (K). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

not provided Benign:1
Apr 16, 2018
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.081
BayesDel_addAF
Benign
-0.80
T
BayesDel_noAF
Benign
-0.92
CADD
Benign
0.022
DANN
Benign
0.50
DEOGEN2
Benign
0.019
.;T
FATHMM_MKL
Benign
0.017
N
LIST_S2
Benign
0.36
T;T
MetaRNN
Benign
0.0055
T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
0.0
.;N
PrimateAI
Benign
0.32
T
PROVEAN
Benign
-0.66
N;N
REVEL
Benign
0.0080
Sift
Benign
0.18
T;T
Sift4G
Uncertain
0.048
D;T
Polyphen
0.029
.;B
Vest4
0.20
MVP
0.030
MPC
0.22
ClinPred
0.013
T
GERP RS
-6.9
Varity_R
0.052
gMVP
0.13

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: rs143235655; hg19: chrX-107320508; API