12-82896071-A-G
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The NM_152588.3(TMTC2):āc.908A>Gā(p.Lys303Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000465 in 1,613,856 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Likely benign (no stars).
Frequency
Consequence
NM_152588.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 151968Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000243 AC: 61AN: 251464Hom.: 0 AF XY: 0.000177 AC XY: 24AN XY: 135904
GnomAD4 exome AF: 0.0000479 AC: 70AN: 1461888Hom.: 0 Cov.: 31 AF XY: 0.0000385 AC XY: 28AN XY: 727246
GnomAD4 genome AF: 0.0000329 AC: 5AN: 151968Hom.: 0 Cov.: 31 AF XY: 0.0000270 AC XY: 2AN XY: 74204
ClinVar
Submissions by phenotype
TMTC2-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 11, 2023 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at