11-44909757-C-T
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Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_130783.5(TSPAN18):c.116C>T(p.Thr39Ile) variant causes a missense change. The variant allele was found at a frequency of 0.000593 in 1,613,654 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. T39T) has been classified as Likely benign.
Frequency
Genomes: 𝑓 0.0033 ( 6 hom., cov: 33)
Exomes 𝑓: 0.00031 ( 3 hom. )
Consequence
TSPAN18
NM_130783.5 missense
NM_130783.5 missense
Scores
7
11
Clinical Significance
Conservation
PhyloP100: 4.92
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -16 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.009831578).
BP6
Variant 11-44909757-C-T is Benign according to our data. Variant chr11-44909757-C-T is described in ClinVar as [Benign]. Clinvar id is 713410.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS2
High Homozygotes in GnomAd4 at 6 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TSPAN18 | NM_130783.5 | c.116C>T | p.Thr39Ile | missense_variant | 5/10 | ENST00000520358.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TSPAN18 | ENST00000520358.7 | c.116C>T | p.Thr39Ile | missense_variant | 5/10 | 5 | NM_130783.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00330 AC: 503AN: 152220Hom.: 6 Cov.: 33
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GnomAD3 exomes AF: 0.000734 AC: 184AN: 250748Hom.: 2 AF XY: 0.000516 AC XY: 70AN XY: 135650
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GnomAD4 exome AF: 0.000310 AC: 453AN: 1461316Hom.: 3 Cov.: 31 AF XY: 0.000267 AC XY: 194AN XY: 727000
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GnomAD4 genome AF: 0.00331 AC: 504AN: 152338Hom.: 6 Cov.: 33 AF XY: 0.00306 AC XY: 228AN XY: 74486
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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 | Oct 09, 2017 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
.;.;T;.;T;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D;D;D;.;D
MetaRNN
Benign
T;T;T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
.;.;L;.;L;.
MutationTaster
Benign
D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;N;N;N;N
REVEL
Uncertain
Sift
Benign
T;T;T;T;T;T
Sift4G
Benign
T;T;T;T;T;T
Polyphen
0.70
.;.;P;.;P;.
Vest4
0.80, 0.80
MVP
MPC
0.51
ClinPred
T
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Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at