1-205241838-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_014858.4(TMCC2):c.541C>T(p.Arg181Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000231 in 1,599,538 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_014858.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TMCC2 | ENST00000358024.8 | c.541C>T | p.Arg181Trp | missense_variant | Exon 2 of 5 | 1 | NM_014858.4 | ENSP00000350718.3 | ||
TMCC2 | ENST00000545499.5 | c.307C>T | p.Arg103Trp | missense_variant | Exon 2 of 5 | 2 | ENSP00000437943.1 | |||
TMCC2 | ENST00000495538.5 | n.772C>T | non_coding_transcript_exon_variant | Exon 2 of 5 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152192Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000235 AC: 5AN: 212522Hom.: 0 AF XY: 0.0000256 AC XY: 3AN XY: 117380
GnomAD4 exome AF: 0.0000214 AC: 31AN: 1447346Hom.: 0 Cov.: 31 AF XY: 0.0000195 AC XY: 14AN XY: 719156
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152192Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74350
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.541C>T (p.R181W) alteration is located in exon 2 (coding exon 2) of the TMCC2 gene. This alteration results from a C to T substitution at nucleotide position 541, causing the arginine (R) at amino acid position 181 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