22-18124178-C-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 0P and 3B. BP4_ModerateBP6
The NM_018943.3(TUBA8):c.249C>T(p.Tyr83=) variant causes a synonymous change. The variant allele was found at a frequency of 0.00013 in 1,614,064 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: 𝑓 0.000066 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00014 ( 1 hom. )
Consequence
TUBA8
NM_018943.3 synonymous
NM_018943.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 4.14
Genes affected
TUBA8 (HGNC:12410): (tubulin alpha 8) This gene encodes a member of the alpha tubulin protein family. Alpha tubulins are one of two core protein families (alpha and beta tubulins) that heterodimerize and assemble to form microtubules. Mutations in this gene are associated with polymicrogyria and optic nerve hypoplasia. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Jul 2010]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -3 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.39).
BP6
?
Variant 22-18124178-C-T is Benign according to our data. Variant chr22-18124178-C-T is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 437123.We mark this variant Likely_benign, oryginal submissions are: {Likely_benign=1, Uncertain_significance=1}.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TUBA8 | NM_018943.3 | c.249C>T | p.Tyr83= | synonymous_variant | 3/5 | ENST00000330423.8 | |
TUBA8 | NM_001193414.2 | c.51C>T | p.Tyr17= | synonymous_variant | 3/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TUBA8 | ENST00000330423.8 | c.249C>T | p.Tyr83= | synonymous_variant | 3/5 | 1 | NM_018943.3 | P1 | |
ENST00000623543.1 | n.6977G>A | non_coding_transcript_exon_variant | 1/1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000657 AC: 10AN: 152182Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000223 AC: 56AN: 251460Hom.: 1 AF XY: 0.000353 AC XY: 48AN XY: 135906
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GnomAD4 exome AF: 0.000137 AC: 200AN: 1461882Hom.: 1 Cov.: 30 AF XY: 0.000188 AC XY: 137AN XY: 727244
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ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:1Benign:1
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Feb 28, 2017 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 27, 2024 | - - |
Computational scores
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BayesDel_noAF
Benign
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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