22-50233406-C-A
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Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_020461.4(TUBGCP6):c.1026G>T(p.Pro342Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
Consequence
TUBGCP6
NM_020461.4 synonymous
NM_020461.4 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -4.22
Genes affected
TUBGCP6 (HGNC:18127): (tubulin gamma complex component 6) The protein encoded by this gene is part of a large multisubunit complex required for microtubule nucleation at the centrosome. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.69).
BP7
Synonymous conserved (PhyloP=-4.22 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TUBGCP6 | NM_020461.4 | c.1026G>T | p.Pro342Pro | synonymous_variant | 3/25 | ENST00000248846.10 | NP_065194.3 | |
TUBGCP6 | XR_001755343.3 | n.1590G>T | non_coding_transcript_exon_variant | 3/20 | ||||
TUBGCP6 | XR_007067982.1 | n.1590G>T | non_coding_transcript_exon_variant | 3/19 | ||||
TUBGCP6 | XR_938347.3 | n.1590G>T | non_coding_transcript_exon_variant | 3/23 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TUBGCP6 | ENST00000248846.10 | c.1026G>T | p.Pro342Pro | synonymous_variant | 3/25 | 1 | NM_020461.4 | ENSP00000248846.5 | ||
TUBGCP6 | ENST00000439308.6 | c.1026G>T | p.Pro342Pro | synonymous_variant | 3/25 | 1 | ENSP00000397387.2 | |||
TUBGCP6 | ENST00000498611.5 | n.1559G>T | non_coding_transcript_exon_variant | 3/23 | 1 | |||||
TUBGCP6 | ENST00000434349.1 | c.255G>T | p.Pro85Pro | synonymous_variant | 2/6 | 5 | ENSP00000409650.1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 genomes
Cov.:
33
GnomAD4 exome Cov.: 32
GnomAD4 exome
Cov.:
32
GnomAD4 genome Cov.: 33
GnomAD4 genome
Cov.:
33
Bravo
AF:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at