12-125350286-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001366854.1(TMEM132B):c.902C>T(p.Thr301Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000471 in 1,613,748 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T301A) has been classified as Uncertain significance.
Frequency
Consequence
NM_001366854.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TMEM132B | NM_001366854.1 | c.902C>T | p.Thr301Met | missense_variant | 2/9 | ENST00000682704.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMEM132B | ENST00000682704.1 | c.902C>T | p.Thr301Met | missense_variant | 2/9 | NM_001366854.1 | P2 | ||
TMEM132B | ENST00000299308.7 | c.887C>T | p.Thr296Met | missense_variant | 2/9 | 5 | A2 | ||
TMEM132B | ENST00000534945.2 | n.835C>T | non_coding_transcript_exon_variant | 1/4 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000657 AC: 10AN: 152160Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000162 AC: 4AN: 246324Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 133994
GnomAD4 exome AF: 0.0000452 AC: 66AN: 1461588Hom.: 0 Cov.: 35 AF XY: 0.0000399 AC XY: 29AN XY: 727064
GnomAD4 genome ? AF: 0.0000657 AC: 10AN: 152160Hom.: 0 Cov.: 33 AF XY: 0.0000673 AC XY: 5AN XY: 74332
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 01, 2022 | The c.887C>T (p.T296M) alteration is located in exon 2 (coding exon 2) of the TMEM132B gene. This alteration results from a C to T substitution at nucleotide position 887, causing the threonine (T) at amino acid position 296 to be replaced by a methionine (M). 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