rs149152116
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The ENST00000425018.1(TUBGCP6):c.1165C>T(p.Arg389Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00313 in 1,612,482 control chromosomes in the GnomAD database, including 13 homozygotes. In-silico tool predicts a benign outcome for this variant. 10/14 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R389H) has been classified as Uncertain significance.
Frequency
Consequence
ENST00000425018.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TUBGCP6 | NM_020461.4 | c.5139C>T | p.His1713= | synonymous_variant | 23/25 | ENST00000248846.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TUBGCP6 | ENST00000248846.10 | c.5139C>T | p.His1713= | synonymous_variant | 23/25 | 1 | NM_020461.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00204 AC: 311AN: 152202Hom.: 2 Cov.: 33
GnomAD3 exomes AF: 0.00210 AC: 523AN: 249006Hom.: 0 AF XY: 0.00217 AC XY: 293AN XY: 135040
GnomAD4 exome AF: 0.00325 AC: 4743AN: 1460162Hom.: 11 Cov.: 37 AF XY: 0.00319 AC XY: 2318AN XY: 726422
GnomAD4 genome ? AF: 0.00204 AC: 311AN: 152320Hom.: 2 Cov.: 33 AF XY: 0.00191 AC XY: 142AN XY: 74480
ClinVar
Submissions by phenotype
not provided Benign:4
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 25, 2024 | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 02, 2021 | - - |
Likely benign, no assertion criteria provided | clinical testing | Clinical Genetics, Academic Medical Center | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2024 | TUBGCP6: BP4, BP7 - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Jul 16, 2018 | - - |
Microcephaly and chorioretinopathy 1 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | Jun 28, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at