chr10-94402971-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_015188.2(TBC1D12):c.358G>A(p.Ala120Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000425 in 1,575,328 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_015188.2 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 |
---|---|---|---|---|---|---|---|
TBC1D12 | NM_015188.2 | c.358G>A | p.Ala120Thr | missense_variant | 1/13 | ENST00000225235.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TBC1D12 | ENST00000225235.5 | c.358G>A | p.Ala120Thr | missense_variant | 1/13 | 1 | NM_015188.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000724 AC: 11AN: 152006Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000432 AC: 8AN: 185214Hom.: 0 AF XY: 0.0000575 AC XY: 6AN XY: 104314
GnomAD4 exome AF: 0.0000393 AC: 56AN: 1423214Hom.: 0 Cov.: 30 AF XY: 0.0000368 AC XY: 26AN XY: 707186
GnomAD4 genome AF: 0.0000723 AC: 11AN: 152114Hom.: 0 Cov.: 33 AF XY: 0.0000538 AC XY: 4AN XY: 74372
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 17, 2021 | The c.358G>A (p.A120T) alteration is located in exon 1 (coding exon 1) of the TBC1D12 gene. This alteration results from a G to A substitution at nucleotide position 358, causing the alanine (A) at amino acid position 120 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at