1-165743252-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_019026.6(TMCO1):āc.383T>Cā(p.Leu128Pro) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000013 in 1,613,832 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_019026.6 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TMCO1 | NM_019026.6 | c.383T>C | p.Leu128Pro | missense_variant | Exon 6 of 7 | ENST00000367881.11 | NP_061899.3 | |
TMCO1 | NM_001256164.1 | c.434T>C | p.Leu145Pro | missense_variant | Exon 6 of 7 | NP_001243093.1 | ||
TMCO1 | NM_001256165.1 | c.347T>C | p.Leu116Pro | missense_variant | Exon 6 of 7 | NP_001243094.1 | ||
TMCO1 | NR_045818.1 | n.477T>C | non_coding_transcript_exon_variant | Exon 6 of 7 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152092Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251418Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135876
GnomAD4 exome AF: 0.0000137 AC: 20AN: 1461740Hom.: 0 Cov.: 31 AF XY: 0.0000151 AC XY: 11AN XY: 727174
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152092Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74302
ClinVar
Submissions by phenotype
not provided Uncertain:1
Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at