2-131480409-C-T
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Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 3P and 4B. PP2PP3_ModerateBS2
The NM_080386.4(TUBA3D):c.716C>T(p.Thr239Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000012 in 1,588,476 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000028 ( 0 hom., cov: 30)
Exomes 𝑓: 0.000010 ( 0 hom. )
Consequence
TUBA3D
NM_080386.4 missense
NM_080386.4 missense
Scores
2
4
8
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 3.26
Genes affected
TUBA3D (HGNC:24071): (tubulin alpha 3d) This gene encodes a member of the alpha tubulin family. Tubulin is a major component of microtubules, which are composed of alpha- and beta-tubulin heterodimers and microtubule-associated proteins in the cytoskeleton. Microtubules maintain cellular structure, function in intracellular transport, and play a role in spindle formation during mitosis. [provided by RefSeq, Oct 2011]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -1 ACMG points.
PP2
Missense variant where missense usually causes diseases, TUBA3D
PP3
MetaRNN computational evidence supports a deleterious effect, 0.843
BS2
High AC in GnomAdExome4 at 15 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TUBA3D | NM_080386.4 | c.716C>T | p.Thr239Ile | missense_variant | 4/5 | ENST00000321253.7 | |
MZT2A | XM_005263742.4 | c.320-8227G>A | intron_variant | ||||
MZT2A | XM_047445568.1 | c.623-8227G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TUBA3D | ENST00000321253.7 | c.716C>T | p.Thr239Ile | missense_variant | 4/5 | 1 | NM_080386.4 | P1 | |
MZT2A | ENST00000427024.5 | c.279-8227G>A | intron_variant, NMD_transcript_variant | 3 | |||||
MZT2A | ENST00000445782.2 | n.331-8227G>A | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000283 AC: 4AN: 141516Hom.: 0 Cov.: 30
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GnomAD3 exomes AF: 0.0000204 AC: 5AN: 245178Hom.: 1 AF XY: 0.0000150 AC XY: 2AN XY: 132964
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GnomAD4 exome AF: 0.0000104 AC: 15AN: 1446960Hom.: 0 Cov.: 38 AF XY: 0.00000694 AC XY: 5AN XY: 720300
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GnomAD4 genome AF: 0.0000283 AC: 4AN: 141516Hom.: 0 Cov.: 30 AF XY: 0.0000433 AC XY: 3AN XY: 69208
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
D
M_CAP
Benign
T
MetaRNN
Pathogenic
D
MetaSVM
Uncertain
T
MutationTaster
Benign
D
PrimateAI
Pathogenic
T
PROVEAN
Uncertain
D
REVEL
Uncertain
Sift4G
Uncertain
D
Vest4
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T
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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