10-47121-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 4P and 1B. PM2PP2PP5BP4
The NM_177987.3(TUBB8):c.1271A>G(p.Gln424Arg) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 11/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (no stars).
Frequency
Genomes: not found (cov: 24)
Consequence
TUBB8
NM_177987.3 missense
NM_177987.3 missense
Scores
5
11
Clinical Significance
Conservation
PhyloP100: 5.67
Genes affected
TUBB8 (HGNC:20773): (tubulin beta 8 class VIII) The protein encoded by this gene represents the primary beta-tubulin subunit of oocytes and the early embryo. Defects in this gene, which is primate-specific, are a cause of oocyte maturation defect 2 and infertility. [provided by RefSeq, Mar 2016]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 3 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
PP2
?
Missense variant where missense usually causes diseases, TUBB8
PP5
?
Variant 10-47121-T-C is Pathogenic according to our data. Variant chr10-47121-T-C is described in ClinVar as [Likely_pathogenic]. Clinvar id is 977661.Status of the report is no_assertion_criteria_provided, 0 stars.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.38418928).. Strength limited to SUPPORTING due to the PP5.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TUBB8 | NM_177987.3 | c.1271A>G | p.Gln424Arg | missense_variant | 4/4 | ENST00000568584.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TUBB8 | ENST00000568584.6 | c.1271A>G | p.Gln424Arg | missense_variant | 4/4 | 1 | NM_177987.3 | P1 | |
TUBB8 | ENST00000564130.2 | c.1169A>G | p.Gln390Arg | missense_variant | 4/4 | 5 | |||
TUBB8 | ENST00000568866.5 | c.1160A>G | p.Gln387Arg | missense_variant | 3/3 | 5 | |||
TUBB8 | ENST00000561967.1 | c.*934A>G | 3_prime_UTR_variant | 4/4 | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 24
GnomAD3 genomes
?
Cov.:
24
GnomAD4 exome Cov.: 23
GnomAD4 exome
Cov.:
23
GnomAD4 genome ? Cov.: 24
GnomAD4 genome
?
Cov.:
24
ClinVar
Significance: Likely pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Oocyte maturation defect 2 Pathogenic:1
Likely pathogenic, no assertion criteria provided | case-control | Center for Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong University | Aug 31, 2020 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
D
LIST_S2
Uncertain
D;D;D
M_CAP
Benign
D
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
D;N;N;N;N
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;N
Sift
Uncertain
D;.;.
Sift4G
Uncertain
D;D;D
Polyphen
0.061
.;.;B
Vest4
MutPred
0.36
.;.;Gain of helix (P = 0.0854);
MVP
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at