chr2-131480159-C-T
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BP4
The NM_080386.4(TUBA3D):c.466C>T(p.Arg156Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R156Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_080386.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TUBA3D | NM_080386.4 | c.466C>T | p.Arg156Trp | missense_variant | Exon 4 of 5 | ENST00000321253.7 | NP_525125.2 | |
MZT2A | XM_047445568.1 | c.623-7977G>A | intron_variant | Intron 1 of 2 | XP_047301524.1 | |||
MZT2A | XM_005263742.4 | c.320-7977G>A | intron_variant | Intron 2 of 3 | XP_005263799.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TUBA3D | ENST00000321253.7 | c.466C>T | p.Arg156Trp | missense_variant | Exon 4 of 5 | 1 | NM_080386.4 | ENSP00000326042.6 | ||
TUBA3D | ENST00000409047.2 | n.292C>T | non_coding_transcript_exon_variant | Exon 3 of 3 | 2 | |||||
MZT2A | ENST00000427024.5 | n.278-7977G>A | intron_variant | Intron 2 of 4 | 3 | ENSP00000403353.1 | ||||
MZT2A | ENST00000445782.2 | n.331-7977G>A | intron_variant | Intron 2 of 3 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 184AN: 135284Hom.: 0 Cov.: 31 FAILED QC
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00105 AC: 1515AN: 1439656Hom.: 0 Cov.: 70 AF XY: 0.00103 AC XY: 739AN XY: 715826
GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00135 AC: 183AN: 135386Hom.: 0 Cov.: 31 AF XY: 0.00155 AC XY: 102AN XY: 65632
ClinVar
Submissions by phenotype
Hepatocellular carcinoma Pathogenic:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at