9-126340561-G-A
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6BP7BA1
The NM_033446.3(MVB12B):c.135G>A(p.Thr45Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.32 in 1,613,512 control chromosomes in the GnomAD database, including 83,933 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Consequence
NM_033446.3 synonymous
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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MVB12B | NM_033446.3 | c.135G>A | p.Thr45Thr | synonymous_variant | Exon 2 of 10 | ENST00000361171.8 | NP_258257.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MVB12B | ENST00000361171.8 | c.135G>A | p.Thr45Thr | synonymous_variant | Exon 2 of 10 | 2 | NM_033446.3 | ENSP00000354772.3 | ||
MVB12B | ENST00000489637.3 | c.135G>A | p.Thr45Thr | synonymous_variant | Exon 2 of 6 | 1 | ENSP00000485994.1 | |||
MVB12B | ENST00000402437.2 | c.90G>A | p.Thr30Thr | synonymous_variant | Exon 2 of 6 | 3 | ENSP00000384751.2 |
Frequencies
GnomAD3 genomes AF: 0.330 AC: 50094AN: 151984Hom.: 8353 Cov.: 33
GnomAD3 exomes AF: 0.323 AC: 81233AN: 251450Hom.: 13482 AF XY: 0.319 AC XY: 43345AN XY: 135898
GnomAD4 exome AF: 0.319 AC: 466914AN: 1461410Hom.: 75576 Cov.: 34 AF XY: 0.318 AC XY: 231052AN XY: 727012
GnomAD4 genome AF: 0.329 AC: 50116AN: 152102Hom.: 8357 Cov.: 33 AF XY: 0.331 AC XY: 24614AN XY: 74332
ClinVar
Submissions by phenotype
MVB12B-related disorder Benign:1
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