9-126503167-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.874-10G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000342 in 1,549,544 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.874-10G>A | intron_variant | Intron 9 of 9 | ENST00000361171.8 | NP_258257.1 | ||
MVB12B | XM_005252297.1 | c.829-10G>A | intron_variant | Intron 9 of 9 | XP_005252354.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152176Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.00000649 AC: 1AN: 154060Hom.: 0 AF XY: 0.0000123 AC XY: 1AN XY: 81352
GnomAD4 exome AF: 0.0000365 AC: 51AN: 1397368Hom.: 0 Cov.: 32 AF XY: 0.0000363 AC XY: 25AN XY: 689322
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152176Hom.: 0 Cov.: 34 AF XY: 0.00 AC XY: 0AN XY: 74342
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