22-50221466-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_020461.4(TUBGCP6):c.2893C>T(p.Pro965Ser) variant causes a missense 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. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P965L) has been classified as Uncertain significance.
Frequency
Consequence
NM_020461.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TUBGCP6 | NM_020461.4 | c.2893C>T | p.Pro965Ser | missense_variant | 16/25 | ENST00000248846.10 | |
TUBGCP6 | XR_001755343.3 | n.3457C>T | non_coding_transcript_exon_variant | 16/20 | |||
TUBGCP6 | XR_938347.3 | n.3457C>T | non_coding_transcript_exon_variant | 16/23 | |||
TUBGCP6 | XR_007067982.1 | n.3048+562C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TUBGCP6 | ENST00000248846.10 | c.2893C>T | p.Pro965Ser | missense_variant | 16/25 | 1 | NM_020461.4 | P1 | |
TUBGCP6 | ENST00000439308.6 | c.2893C>T | p.Pro965Ser | missense_variant | 16/25 | 1 | |||
TUBGCP6 | ENST00000498611.5 | n.3426C>T | non_coding_transcript_exon_variant | 16/23 | 1 | ||||
TUBGCP6 | ENST00000491449.5 | n.1200C>T | non_coding_transcript_exon_variant | 8/16 | 5 |
Frequencies
GnomAD3 genomes Cov.: 34
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1440966Hom.: 0 Cov.: 36 AF XY: 0.00 AC XY: 0AN XY: 715714
GnomAD4 genome Cov.: 34
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Jul 24, 2015 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at