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):ā€‹c.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

Genomes: not found (cov: 32)
Exomes š‘“: 0.000014 ( 0 hom. )

Consequence

TOMT
NM_001393500.2 missense

Scores

1
18

Clinical Significance

Uncertain significance criteria provided, multiple submitters, no conflicts U:2

Conservation

PhyloP100: 1.44
Variant links:
Genes affected
TOMT (HGNC:55527): (transmembrane O-methyltransferase) This gene encodes a catechol-O-methyltransferase that catalyzes the transfer of a methyl group from S-adenosyl-L-methionine to a hydroxyl group of catechols and is essential for auditory and vestibular function. Mutations in this gene have been associated with nonsyndromic deafness. Readthrough transcription is observed across this gene and the adjacent leucine-rich repeat containing 51 gene. A third locus (GeneID:220074) is defined to represent the readthrough transcripts. [provided by RefSeq, Feb 2021]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.16880006).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
TOMTNM_001393500.2 linkuse as main transcriptc.97C>G p.Leu33Val missense_variant 1/3 ENST00000541899.3 NP_001380429.1
LRTOMTNM_001145309.4 linkuse as main transcriptc.196C>G p.Leu66Val missense_variant 7/9 NP_001138781.1
LRTOMTNM_001145308.5 linkuse as main transcriptc.196C>G p.Leu66Val missense_variant 5/7 NP_001138780.1
LRTOMTNM_001145310.4 linkuse as main transcriptc.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
TOMTENST00000541899.3 linkuse as main transcriptc.97C>G p.Leu33Val missense_variant 1/35 NM_001393500.2 ENSP00000494667 P1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD3 exomes
AF:
0.0000129
AC:
2
AN:
154530
Hom.:
0
AF XY:
0.0000244
AC XY:
2
AN XY:
82086
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000167
Gnomad OTH exome
AF:
0.000229
GnomAD4 exome
AF:
0.0000136
AC:
19
AN:
1398688
Hom.:
0
Cov.:
31
AF XY:
0.0000159
AC XY:
11
AN XY:
689912
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000176
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32
Alfa
AF:
0.0000282
Hom.:
0
Bravo
AF:
0.00000378

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingLaboratory for Molecular Medicine, Mass General Brigham Personalized MedicineJun 11, 2015Variant 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 submitterclinical testingIllumina Laboratory Services, IlluminaJan 12, 2018This 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: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.096
BayesDel_addAF
Benign
-0.14
T
BayesDel_noAF
Benign
-0.34
CADD
Benign
14
DANN
Benign
0.92
DEOGEN2
Benign
0.046
T;T;.
Eigen
Benign
-0.57
Eigen_PC
Benign
-0.40
FATHMM_MKL
Benign
0.66
D
LIST_S2
Benign
0.67
T;.;T
M_CAP
Benign
0.067
D
MetaRNN
Benign
0.17
T;T;T
MetaSVM
Benign
-0.55
T
MutationAssessor
Benign
0.69
N;N;.
MutationTaster
Benign
1.0
D;D;N;N
PrimateAI
Uncertain
0.56
T
PROVEAN
Benign
-0.21
N;N;.
REVEL
Benign
0.16
Sift
Benign
0.30
T;T;.
Sift4G
Benign
0.63
T;T;.
Polyphen
0.0010
B;B;.
Vest4
0.15
MutPred
0.33
Gain of MoRF binding (P = 0.1109);Gain of MoRF binding (P = 0.1109);.;
MVP
0.77
MPC
0.11
ClinPred
0.095
T
GERP RS
3.5
Varity_R
0.052
gMVP
0.54

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs876657864; hg19: chr11-71817094; API