rs3763978
Positions:
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1
The NM_004616.3(TSPAN8):āc.218G>Cā(p.Gly73Ala) variant causes a missense change. The variant allele was found at a frequency of 0.373 in 1,612,202 control chromosomes in the GnomAD database, including 118,156 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in Lovd as Benign (no stars). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Genomes: š 0.29 ( 7969 hom., cov: 32)
Exomes š: 0.38 ( 110187 hom. )
Consequence
TSPAN8
NM_004616.3 missense
NM_004616.3 missense
Scores
7
5
5
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 4.68
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 -13 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0057137907).
BP6
?
Variant 12-71139754-C-G is Benign according to our data. Variant chr12-71139754-C-G is described in Lovd as [Benign].
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.404 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TSPAN8 | NM_004616.3 | c.218G>C | p.Gly73Ala | missense_variant | 4/9 | ENST00000247829.8 | |
TSPAN8 | NM_001369760.1 | c.218G>C | p.Gly73Ala | missense_variant | 3/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TSPAN8 | ENST00000247829.8 | c.218G>C | p.Gly73Ala | missense_variant | 4/9 | 1 | NM_004616.3 | P1 | |
TSPAN8 | ENST00000393330.6 | c.218G>C | p.Gly73Ala | missense_variant | 7/12 | 1 | P1 | ||
TSPAN8 | ENST00000546561.2 | c.218G>C | p.Gly73Ala | missense_variant | 3/8 | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.294 AC: 44603AN: 151926Hom.: 7967 Cov.: 32
GnomAD3 genomes
?
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GnomAD3 exomes AF: 0.329 AC: 82526AN: 250554Hom.: 15208 AF XY: 0.342 AC XY: 46266AN XY: 135422
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GnomAD4 exome AF: 0.381 AC: 556859AN: 1460158Hom.: 110187 Cov.: 41 AF XY: 0.381 AC XY: 276909AN XY: 726328
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GnomAD4 genome ? AF: 0.293 AC: 44601AN: 152044Hom.: 7969 Cov.: 32 AF XY: 0.290 AC XY: 21544AN XY: 74326
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ESP6500AA
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ExAC
?
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40448
Asia WGS
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881
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3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Benign
T
BayesDel_noAF
Uncertain
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Uncertain
T;T;T
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Uncertain
D
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationAssessor
Pathogenic
H;H;H
MutationTaster
Benign
P;P;P
PrimateAI
Uncertain
T
PROVEAN
Pathogenic
D;D;D
REVEL
Pathogenic
Sift
Benign
D;D;D
Sift4G
Pathogenic
D;D;D
Polyphen
D;D;D
Vest4
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