9-126392159-G-A
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_033446.3(MVB12B):c.503G>A(p.Arg168Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000124 in 1,614,040 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_033446.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MVB12B | NM_033446.3 | c.503G>A | p.Arg168Gln | missense_variant | Exon 5 of 10 | ENST00000361171.8 | NP_258257.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MVB12B | ENST00000361171.8 | c.503G>A | p.Arg168Gln | missense_variant | Exon 5 of 10 | 2 | NM_033446.3 | ENSP00000354772.3 | ||
MVB12B | ENST00000489637.3 | c.503G>A | p.Arg168Gln | missense_variant | Exon 5 of 6 | 1 | ENSP00000485994.1 | |||
MVB12B | ENST00000402437.2 | c.458G>A | p.Arg153Gln | missense_variant | Exon 5 of 6 | 3 | ENSP00000384751.2 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152174Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251476Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135914
GnomAD4 exome AF: 0.0000123 AC: 18AN: 1461866Hom.: 0 Cov.: 31 AF XY: 0.0000110 AC XY: 8AN XY: 727240
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152174Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74346
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.503G>A (p.R168Q) alteration is located in exon 5 (coding exon 5) of the MVB12B gene. This alteration results from a G to A substitution at nucleotide position 503, causing the arginine (R) at amino acid position 168 to be replaced by a glutamine (Q). 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