chr11-44909729-A-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_130783.5(TSPAN18):​c.88A>T​(p.Ile30Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000113 in 1,612,188 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.00033 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000090 ( 1 hom. )

Consequence

TSPAN18
NM_130783.5 missense

Scores

5
14

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.180
Variant links:
Genes affected
TSPAN18 (HGNC:20660): (tetraspanin 18) Predicted to be integral component of membrane. Predicted to be integral component of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]
TP53I11 (HGNC:16842): (tumor protein p53 inducible protein 11) Predicted to be involved in negative regulation of cell population proliferation. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.08259407).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
TSPAN18NM_130783.5 linkuse as main transcriptc.88A>T p.Ile30Phe missense_variant 5/10 ENST00000520358.7 NP_570139.3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
TSPAN18ENST00000520358.7 linkuse as main transcriptc.88A>T p.Ile30Phe missense_variant 5/105 NM_130783.5 ENSP00000429993 P1

Frequencies

GnomAD3 genomes
AF:
0.000335
AC:
51
AN:
152126
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.000966
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000393
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:
0.0000735
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000132
AC:
33
AN:
249742
Hom.:
1
AF XY:
0.000111
AC XY:
15
AN XY:
135200
show subpopulations
Gnomad AFR exome
AF:
0.00112
Gnomad AMR exome
AF:
0.000116
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:
0.0000882
Gnomad OTH exome
AF:
0.000164
GnomAD4 exome
AF:
0.0000897
AC:
131
AN:
1459944
Hom.:
1
Cov.:
31
AF XY:
0.0000936
AC XY:
68
AN XY:
726326
show subpopulations
Gnomad4 AFR exome
AF:
0.00108
Gnomad4 AMR exome
AF:
0.000179
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:
0.0000648
Gnomad4 OTH exome
AF:
0.000182
GnomAD4 genome
AF:
0.000335
AC:
51
AN:
152244
Hom.:
0
Cov.:
33
AF XY:
0.000376
AC XY:
28
AN XY:
74438
show subpopulations
Gnomad4 AFR
AF:
0.000963
Gnomad4 AMR
AF:
0.000392
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000735
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.0000597
Hom.:
0
Bravo
AF:
0.000502
ESP6500AA
AF:
0.00159
AC:
7
ESP6500EA
AF:
0.00
AC:
0
ExAC
AF:
0.000132
AC:
16
EpiCase
AF:
0.0000545
EpiControl
AF:
0.000178

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsSep 27, 2022The c.88A>T (p.I30F) alteration is located in exon 4 (coding exon 2) of the TSPAN18 gene. This alteration results from a A to T substitution at nucleotide position 88, causing the isoleucine (I) at amino acid position 30 to be replaced by a phenylalanine (F). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.21
BayesDel_addAF
Benign
-0.29
T
BayesDel_noAF
Benign
-0.24
CADD
Benign
8.6
DANN
Benign
0.96
DEOGEN2
Benign
0.34
.;.;T;.;T;.
Eigen
Benign
-0.97
Eigen_PC
Benign
-0.95
FATHMM_MKL
Benign
0.30
N
LIST_S2
Uncertain
0.89
D;D;D;D;.;D
M_CAP
Benign
0.083
D
MetaRNN
Benign
0.083
T;T;T;T;T;T
MetaSVM
Benign
-0.90
T
MutationAssessor
Benign
0.28
.;.;N;.;N;.
MutationTaster
Benign
0.93
D;D
PrimateAI
Benign
0.33
T
PROVEAN
Uncertain
-3.7
D;D;D;D;D;D
REVEL
Uncertain
0.35
Sift
Uncertain
0.0040
D;D;D;D;D;D
Sift4G
Uncertain
0.0050
D;T;D;D;D;D
Polyphen
0.087
.;.;B;.;B;.
Vest4
0.50
MVP
0.18
MPC
0.52
ClinPred
0.080
T
GERP RS
-5.2
Varity_R
0.30
gMVP
0.66

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: rs141764047; hg19: chr11-44931280; COSMIC: COSV99073503; API