rs17256042
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001101312.2(TMEM176B):c.538C>T(p.Arg180Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0426 in 1,614,104 control chromosomes in the GnomAD database, including 1,673 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_001101312.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TMEM176B | NM_001101312.2 | c.538C>T | p.Arg180Trp | missense_variant | 5/7 | ENST00000326442.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMEM176B | ENST00000326442.10 | c.538C>T | p.Arg180Trp | missense_variant | 5/7 | 1 | NM_001101312.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0331 AC: 5038AN: 152140Hom.: 103 Cov.: 32
GnomAD3 exomes AF: 0.0330 AC: 8294AN: 251370Hom.: 171 AF XY: 0.0328 AC XY: 4457AN XY: 135860
GnomAD4 exome AF: 0.0436 AC: 63718AN: 1461846Hom.: 1571 Cov.: 32 AF XY: 0.0430 AC XY: 31259AN XY: 727222
GnomAD4 genome ? AF: 0.0331 AC: 5033AN: 152258Hom.: 102 Cov.: 32 AF XY: 0.0318 AC XY: 2368AN XY: 74432
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at