X-30219227-A-G
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_002364.5(MAGEB2):āc.647A>Gā(p.Asn216Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000108 in 1,209,017 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 4 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_002364.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000897 AC: 1AN: 111449Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 33655
GnomAD3 exomes AF: 0.0000110 AC: 2AN: 182177Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 66675
GnomAD4 exome AF: 0.0000109 AC: 12AN: 1097568Hom.: 0 Cov.: 32 AF XY: 0.0000110 AC XY: 4AN XY: 362934
GnomAD4 genome AF: 0.00000897 AC: 1AN: 111449Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 33655
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.647A>G (p.N216S) alteration is located in exon 2 (coding exon 1) of the MAGEB2 gene. This alteration results from a A to G substitution at nucleotide position 647, causing the asparagine (N) at amino acid position 216 to be replaced by a serine (S). 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