chr15-37936872-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_152453.4(TMCO5A):c.166C>T(p.Arg56Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000682 in 1,611,864 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_152453.4 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 |
---|---|---|---|---|---|---|---|---|
TMCO5A | NM_152453.4 | c.166C>T | p.Arg56Trp | missense_variant | 4/12 | ENST00000319669.5 | NP_689666.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TMCO5A | ENST00000319669.5 | c.166C>T | p.Arg56Trp | missense_variant | 4/12 | 1 | NM_152453.4 | ENSP00000327234 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 151942Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000400 AC: 1AN: 249852Hom.: 0 AF XY: 0.00000740 AC XY: 1AN XY: 135054
GnomAD4 exome AF: 0.00000685 AC: 10AN: 1459922Hom.: 0 Cov.: 31 AF XY: 0.00000964 AC XY: 7AN XY: 726322
GnomAD4 genome AF: 0.00000658 AC: 1AN: 151942Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74178
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 05, 2023 | The c.166C>T (p.R56W) alteration is located in exon 3 (coding exon 2) of the TMCO5A gene. This alteration results from a C to T substitution at nucleotide position 166, causing the arginine (R) at amino acid position 56 to be replaced by a tryptophan (W). 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