chr12-129074541-C-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_133448.3(TMEM132D):c.2634G>T(p.Leu878Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0331 in 1,613,982 control chromosomes in the GnomAD database, including 1,414 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_133448.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TMEM132D | NM_133448.3 | c.2634G>T | p.Leu878Phe | missense_variant | 9/9 | ENST00000422113.7 | |
LOC124903086 | XR_007063612.1 | n.87-365C>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMEM132D | ENST00000422113.7 | c.2634G>T | p.Leu878Phe | missense_variant | 9/9 | 1 | NM_133448.3 | P1 | |
TMEM132D | ENST00000389441.8 | c.1248G>T | p.Leu416Phe | missense_variant | 4/4 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0570 AC: 8670AN: 151978Hom.: 422 Cov.: 32
GnomAD3 exomes AF: 0.0296 AC: 7432AN: 251474Hom.: 264 AF XY: 0.0268 AC XY: 3640AN XY: 135912
GnomAD4 exome AF: 0.0306 AC: 44744AN: 1461886Hom.: 990 Cov.: 30 AF XY: 0.0294 AC XY: 21367AN XY: 727248
GnomAD4 genome ? AF: 0.0571 AC: 8684AN: 152096Hom.: 424 Cov.: 32 AF XY: 0.0559 AC XY: 4154AN XY: 74350
ClinVar
Submissions by phenotype
TMEM132D-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Nov 25, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at