20-2561952-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_080751.3(TMC2):c.496C>T(p.Leu166Phe) variant causes a missense change. The variant allele was found at a frequency of 0.0000105 in 1,614,104 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_080751.3 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 |
---|---|---|---|---|---|---|---|---|
TMC2 | NM_080751.3 | c.496C>T | p.Leu166Phe | missense_variant | Exon 4 of 20 | ENST00000358864.2 | NP_542789.2 | |
TMC2 | XM_005260660.5 | c.571C>T | p.Leu191Phe | missense_variant | Exon 2 of 18 | XP_005260717.1 | ||
TMC2 | XR_001754152.2 | n.705C>T | non_coding_transcript_exon_variant | Exon 2 of 13 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152240Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251396Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135888
GnomAD4 exome AF: 0.00000958 AC: 14AN: 1461864Hom.: 0 Cov.: 30 AF XY: 0.00000963 AC XY: 7AN XY: 727238
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152240Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74386
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.496C>T (p.L166F) alteration is located in exon 4 (coding exon 4) of the TMC2 gene. This alteration results from a C to T substitution at nucleotide position 496, causing the leucine (L) at amino acid position 166 to be replaced by a phenylalanine (F). 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