chr12-125350285-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001366854.1(TMEM132B):c.901A>G(p.Thr301Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000564 in 1,613,838 control chromosomes in the GnomAD database, including 1 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 Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T301M) has been classified as Uncertain significance.
Frequency
Consequence
NM_001366854.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TMEM132B | NM_001366854.1 | c.901A>G | p.Thr301Ala | missense_variant | 2/9 | ENST00000682704.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMEM132B | ENST00000682704.1 | c.901A>G | p.Thr301Ala | missense_variant | 2/9 | NM_001366854.1 | P2 | ||
TMEM132B | ENST00000299308.7 | c.886A>G | p.Thr296Ala | missense_variant | 2/9 | 5 | A2 | ||
TMEM132B | ENST00000534945.2 | n.834A>G | non_coding_transcript_exon_variant | 1/4 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000361 AC: 55AN: 152210Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000203 AC: 5AN: 246460Hom.: 0 AF XY: 0.0000149 AC XY: 2AN XY: 134064
GnomAD4 exome AF: 0.0000246 AC: 36AN: 1461628Hom.: 1 Cov.: 35 AF XY: 0.0000179 AC XY: 13AN XY: 727092
GnomAD4 genome ? AF: 0.000361 AC: 55AN: 152210Hom.: 0 Cov.: 33 AF XY: 0.000417 AC XY: 31AN XY: 74358
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 18, 2021 | The c.886A>G (p.T296A) alteration is located in exon 2 (coding exon 2) of the TMEM132B gene. This alteration results from a A to G substitution at nucleotide position 886, causing the threonine (T) at amino acid position 296 to be replaced by an alanine (A). 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