chr10-47525-A-G
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The NM_177987.3(TUBB8):c.867T>C(p.Leu289=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0031 ( 0 hom., cov: 29)
Exomes 𝑓: 0.00013 ( 1 hom. )
Failed GnomAD Quality Control
Consequence
TUBB8
NM_177987.3 synonymous
NM_177987.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.278
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 Benign. Variant got -7 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.73).
BP6
?
Variant 10-47525-A-G is Benign according to our data. Variant chr10-47525-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 2578610.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-0.278 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TUBB8 | NM_177987.3 | c.867T>C | p.Leu289= | synonymous_variant | 4/4 | ENST00000568584.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TUBB8 | ENST00000568584.6 | c.867T>C | p.Leu289= | synonymous_variant | 4/4 | 1 | NM_177987.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 443AN: 142698Hom.: 0 Cov.: 29 FAILED QC
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29
FAILED QC
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000134 AC: 194AN: 1447580Hom.: 1 Cov.: 32 AF XY: 0.000108 AC XY: 78AN XY: 720002
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Data not reliable, filtered out with message: AS_VQSR
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GnomAD4 genome ? Data not reliable, filtered out with message: AS_VQSR AF: 0.00309 AC: 442AN: 142816Hom.: 0 Cov.: 29 AF XY: 0.00302 AC XY: 211AN XY: 69922
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?
Data not reliable, filtered out with message: AS_VQSR
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2023 | TUBB8: BP4, BS1 - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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