16-2500919-C-T
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS1
The NM_001199107.2(TBC1D24):c.1641C>T(p.Ala547=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000372 in 1,612,734 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. A547A) has been classified as Likely benign.
Frequency
Consequence
NM_001199107.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -17 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TBC1D24 | NM_001199107.2 | c.1641C>T | p.Ala547= | synonymous_variant | 8/8 | ENST00000646147.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TBC1D24 | ENST00000646147.1 | c.1641C>T | p.Ala547= | synonymous_variant | 8/8 | NM_001199107.2 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.000250 AC: 38AN: 152234Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000484 AC: 12AN: 247748Hom.: 0 AF XY: 0.0000668 AC XY: 9AN XY: 134756
GnomAD4 exome AF: 0.0000151 AC: 22AN: 1460500Hom.: 0 Cov.: 31 AF XY: 0.0000165 AC XY: 12AN XY: 726656
GnomAD4 genome ? AF: 0.000250 AC: 38AN: 152234Hom.: 0 Cov.: 33 AF XY: 0.000390 AC XY: 29AN XY: 74366
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 17, 2018 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Developmental and epileptic encephalopathy, 1;C3892048:Autosomal dominant nonsyndromic hearing loss 65;CN236805:Caused by mutation in the TBC1 domain family, member 24 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jul 26, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at