rs571041354
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001127198.5(TMC6):c.475G>A(p.Ala159Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000177 in 1,590,228 control chromosomes in the GnomAD database, including 3 homozygotes. 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 Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. A159A) has been classified as Likely benign.
Frequency
Consequence
NM_001127198.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TMC6 | NM_001127198.5 | c.475G>A | p.Ala159Thr | missense_variant | 6/20 | ENST00000590602.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMC6 | ENST00000590602.6 | c.475G>A | p.Ala159Thr | missense_variant | 6/20 | 2 | NM_001127198.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000105 AC: 16AN: 152250Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000392 AC: 83AN: 211912Hom.: 1 AF XY: 0.000534 AC XY: 61AN XY: 114236
GnomAD4 exome AF: 0.000184 AC: 265AN: 1437860Hom.: 3 Cov.: 33 AF XY: 0.000271 AC XY: 193AN XY: 712942
GnomAD4 genome ? AF: 0.000105 AC: 16AN: 152368Hom.: 0 Cov.: 33 AF XY: 0.000134 AC XY: 10AN XY: 74504
ClinVar
Submissions by phenotype
Epidermodysplasia verruciformis Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Aug 17, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at