rs7424438
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_080386.4(TUBA3D):c.375+30T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0696 in 1,500,604 control chromosomes in the GnomAD database, including 11,571 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.17 ( 3936 hom., cov: 32)
Exomes 𝑓: 0.058 ( 7635 hom. )
Consequence
TUBA3D
NM_080386.4 intron
NM_080386.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.965
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 Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.98).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.408 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TUBA3D | NM_080386.4 | c.375+30T>G | intron_variant | ENST00000321253.7 | |||
MZT2A | XM_005263742.4 | c.320-7304A>C | intron_variant | ||||
MZT2A | XM_047445568.1 | c.623-7304A>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TUBA3D | ENST00000321253.7 | c.375+30T>G | intron_variant | 1 | NM_080386.4 | P1 | |||
MZT2A | ENST00000427024.5 | c.279-7304A>C | intron_variant, NMD_transcript_variant | 3 | |||||
TUBA3D | ENST00000409047.2 | n.201+30T>G | intron_variant, non_coding_transcript_variant | 2 | |||||
MZT2A | ENST00000445782.2 | n.331-7304A>C | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.169 AC: 25537AN: 151360Hom.: 3915 Cov.: 32
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GnomAD3 exomes AF: 0.0581 AC: 13500AN: 232406Hom.: 1613 AF XY: 0.0531 AC XY: 6661AN XY: 125524
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GnomAD4 exome AF: 0.0584 AC: 78801AN: 1349132Hom.: 7635 Cov.: 32 AF XY: 0.0585 AC XY: 39350AN XY: 672228
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GnomAD4 genome ? AF: 0.169 AC: 25594AN: 151472Hom.: 3936 Cov.: 32 AF XY: 0.164 AC XY: 12118AN XY: 74052
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at