11-72106048-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001393500.2(TOMT):āc.97C>Gā(p.Leu33Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000136 in 1,398,688 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 Uncertain significance (ā ā ).
Frequency
Consequence
NM_001393500.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TOMT | NM_001393500.2 | c.97C>G | p.Leu33Val | missense_variant | 1/3 | ENST00000541899.3 | NP_001380429.1 | |
LRTOMT | NM_001145309.4 | c.196C>G | p.Leu66Val | missense_variant | 7/9 | NP_001138781.1 | ||
LRTOMT | NM_001145308.5 | c.196C>G | p.Leu66Val | missense_variant | 5/7 | NP_001138780.1 | ||
LRTOMT | NM_001145310.4 | c.84-8C>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | NP_001138782.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TOMT | ENST00000541899.3 | c.97C>G | p.Leu33Val | missense_variant | 1/3 | 5 | NM_001393500.2 | ENSP00000494667 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000129 AC: 2AN: 154530Hom.: 0 AF XY: 0.0000244 AC XY: 2AN XY: 82086
GnomAD4 exome AF: 0.0000136 AC: 19AN: 1398688Hom.: 0 Cov.: 31 AF XY: 0.0000159 AC XY: 11AN XY: 689912
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Jun 11, 2015 | Variant classified as Uncertain Significance - Favor Benign. The p.Leu66Val vari ant in LRTOMT has not been previously reported in individuals with hearing loss or in large population studies. Leucine (Leu) at position 66 is not conserved th rough species, with multiple birds and fish species having a valine (Val) at thi s position. Additional computational prediction tools suggest that this variant may not impact the protein, though this information is not predictive enough to rule out pathogenicity. In summary, while the clinical significance of the p.Leu 66Val variant is uncertain, the lack of evolutionarily conservation suggests tha t it is more likely to be benign. - |
Autosomal recessive nonsyndromic hearing loss 63 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 12, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at