12-125349641-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001366854.1(TMEM132B):c.257C>A(p.Pro86His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000372 in 1,613,976 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. P86A) 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 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TMEM132B | NM_001366854.1 | c.257C>A | p.Pro86His | missense_variant | 2/9 | ENST00000682704.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMEM132B | ENST00000682704.1 | c.257C>A | p.Pro86His | missense_variant | 2/9 | NM_001366854.1 | P2 | ||
TMEM132B | ENST00000299308.7 | c.242C>A | p.Pro81His | missense_variant | 2/9 | 5 | A2 | ||
TMEM132B | ENST00000534945.2 | n.190C>A | non_coding_transcript_exon_variant | 1/4 | 5 | ||||
TMEM132B | ENST00000535330.1 | n.416C>A | non_coding_transcript_exon_variant | 3/3 | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152088Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000801 AC: 2AN: 249546Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135388
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461888Hom.: 0 Cov.: 52 AF XY: 0.00 AC XY: 0AN XY: 727246
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152088Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74268
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 15, 2023 | The c.242C>A (p.P81H) alteration is located in exon 2 (coding exon 2) of the TMEM132B gene. This alteration results from a C to A substitution at nucleotide position 242, causing the proline (P) at amino acid position 81 to be replaced by a histidine (H). 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