12-82896204-G-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_152588.3(TMTC2):c.1041G>T(p.Gln347His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000198 in 1,614,024 control chromosomes in the GnomAD database, including 3 homozygotes. 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 (★).
Frequency
Consequence
NM_152588.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TMTC2 | NM_152588.3 | c.1041G>T | p.Gln347His | missense_variant | 3/12 | ENST00000321196.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMTC2 | ENST00000321196.8 | c.1041G>T | p.Gln347His | missense_variant | 3/12 | 1 | NM_152588.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00107 AC: 163AN: 152038Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000255 AC: 64AN: 251416Hom.: 0 AF XY: 0.000206 AC XY: 28AN XY: 135882
GnomAD4 exome AF: 0.000107 AC: 157AN: 1461868Hom.: 2 Cov.: 31 AF XY: 0.000107 AC XY: 78AN XY: 727236
GnomAD4 genome ? AF: 0.00107 AC: 163AN: 152156Hom.: 1 Cov.: 32 AF XY: 0.00104 AC XY: 77AN XY: 74380
ClinVar
Submissions by phenotype
TMTC2-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 22, 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