chr12-71139812-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_004616.3(TSPAN8):c.160G>A(p.Val54Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00247 in 1,613,540 control chromosomes in the GnomAD database, including 102 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.013 ( 54 hom., cov: 33)
Exomes 𝑓: 0.0014 ( 48 hom. )
Consequence
TSPAN8
NM_004616.3 missense
NM_004616.3 missense
Scores
17
Clinical Significance
Conservation
PhyloP100: -3.12
Genes affected
TSPAN8 (HGNC:11855): (tetraspanin 8) The protein encoded by this gene is a member of the transmembrane 4 superfamily, also known as the tetraspanin family. Most of these members are cell-surface proteins that are characterized by the presence of four hydrophobic domains. The proteins mediate signal transduction events that play a role in the regulation of cell development, activation, growth and motility. This encoded protein is a cell surface glycoprotein that is known to complex with integrins. This gene is expressed in different carcinomas. The use of alternate polyadenylation sites has been found for this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0035257936).
BP6
?
Variant 12-71139812-C-T is Benign according to our data. Variant chr12-71139812-C-T is described in ClinVar as [Benign]. Clinvar id is 710174.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.013 (1976/152234) while in subpopulation AFR AF= 0.0448 (1859/41528). AF 95% confidence interval is 0.0431. There are 54 homozygotes in gnomad4. There are 919 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 53 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TSPAN8 | NM_004616.3 | c.160G>A | p.Val54Ile | missense_variant | 4/9 | ENST00000247829.8 | |
TSPAN8 | NM_001369760.1 | c.160G>A | p.Val54Ile | missense_variant | 3/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TSPAN8 | ENST00000247829.8 | c.160G>A | p.Val54Ile | missense_variant | 4/9 | 1 | NM_004616.3 | P1 | |
TSPAN8 | ENST00000393330.6 | c.160G>A | p.Val54Ile | missense_variant | 7/12 | 1 | P1 | ||
TSPAN8 | ENST00000546561.2 | c.160G>A | p.Val54Ile | missense_variant | 3/8 | 1 | P1 | ||
TSPAN8 | ENST00000552786.1 | downstream_gene_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0130 AC: 1974AN: 152116Hom.: 53 Cov.: 33
GnomAD3 genomes
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GnomAD3 exomes AF: 0.00354 AC: 888AN: 250826Hom.: 27 AF XY: 0.00255 AC XY: 345AN XY: 135554
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GnomAD4 exome AF: 0.00138 AC: 2010AN: 1461306Hom.: 48 Cov.: 32 AF XY: 0.00114 AC XY: 831AN XY: 726974
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GnomAD4 genome ? AF: 0.0130 AC: 1976AN: 152234Hom.: 54 Cov.: 33 AF XY: 0.0123 AC XY: 919AN XY: 74434
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ESP6500AA
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197
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ExAC
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543
Asia WGS
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3478
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jun 14, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
DEOGEN2
Benign
T;T;T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
N;N;N
MutationTaster
Benign
N;N;N
PrimateAI
Benign
T
PROVEAN
Benign
N;N;N
REVEL
Benign
Sift
Benign
T;T;T
Sift4G
Benign
T;T;T
Polyphen
B;B;B
Vest4
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
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