13-113495690-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_017905.6(TMCO3):c.109C>T(p.Arg37Cys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000143 in 1,612,154 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R37H) has been classified as Uncertain significance.
Frequency
Consequence
NM_017905.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TMCO3 | NM_017905.6 | c.109C>T | p.Arg37Cys | missense_variant | Exon 2 of 13 | ENST00000434316.7 | NP_060375.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TMCO3 | ENST00000434316.7 | c.109C>T | p.Arg37Cys | missense_variant | Exon 2 of 13 | 1 | NM_017905.6 | ENSP00000389399.2 | ||
TMCO3 | ENST00000375391.5 | c.109C>T | p.Arg37Cys | missense_variant | Exon 2 of 8 | 1 | ENSP00000364540.1 | |||
TMCO3 | ENST00000474393.5 | c.109C>T | p.Arg37Cys | missense_variant | Exon 2 of 9 | 2 | ENSP00000484053.1 | |||
TMCO3 | ENST00000473287.1 | c.-183C>T | upstream_gene_variant | 2 | ENSP00000478818.1 |
Frequencies
GnomAD3 genomes AF: 0.0000920 AC: 14AN: 152122Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000168 AC: 42AN: 249954Hom.: 0 AF XY: 0.000170 AC XY: 23AN XY: 135354
GnomAD4 exome AF: 0.000149 AC: 217AN: 1460032Hom.: 0 Cov.: 32 AF XY: 0.000134 AC XY: 97AN XY: 725978
GnomAD4 genome AF: 0.0000920 AC: 14AN: 152122Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74310
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.109C>T (p.R37C) alteration is located in exon 2 (coding exon 1) of the TMCO3 gene. This alteration results from a C to T substitution at nucleotide position 109, causing the arginine (R) at amino acid position 37 to be replaced by a cysteine (C). 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