9-126483963-G-A
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The NM_033446.3(MVB12B):c.814-10G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000874 in 1,614,046 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_033446.3 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MVB12B | NM_033446.3 | c.814-10G>A | intron_variant | Intron 8 of 9 | ENST00000361171.8 | NP_258257.1 | ||
MVB12B | XM_005252297.1 | c.769-10G>A | intron_variant | Intron 8 of 9 | XP_005252354.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000539 AC: 82AN: 152222Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000107 AC: 27AN: 251382Hom.: 0 AF XY: 0.0000810 AC XY: 11AN XY: 135860
GnomAD4 exome AF: 0.0000404 AC: 59AN: 1461706Hom.: 0 Cov.: 31 AF XY: 0.0000261 AC XY: 19AN XY: 727160
GnomAD4 genome AF: 0.000538 AC: 82AN: 152340Hom.: 0 Cov.: 33 AF XY: 0.000524 AC XY: 39AN XY: 74496
ClinVar
Submissions by phenotype
MVB12B-related disorder Benign:1
This variant is classified as likely 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