X-30218696-C-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_002364.5(MAGEB2):c.116C>A(p.Pro39His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000181 in 1,203,529 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 63 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002364.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000891 AC: 10AN: 112296Hom.: 0 Cov.: 23 AF XY: 0.0000870 AC XY: 3AN XY: 34468
GnomAD3 exomes AF: 0.0000712 AC: 12AN: 168434Hom.: 0 AF XY: 0.0000364 AC XY: 2AN XY: 54876
GnomAD4 exome AF: 0.000191 AC: 208AN: 1091181Hom.: 0 Cov.: 31 AF XY: 0.000168 AC XY: 60AN XY: 357207
GnomAD4 genome AF: 0.0000890 AC: 10AN: 112348Hom.: 0 Cov.: 23 AF XY: 0.0000869 AC XY: 3AN XY: 34530
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.116C>A (p.P39H) alteration is located in exon 2 (coding exon 1) of the MAGEB2 gene. This alteration results from a C to A substitution at nucleotide position 116, causing the proline (P) at amino acid position 39 to be replaced by a histidine (H). 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