X-30218598-G-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_002364.5(MAGEB2):c.18G>T(p.Lys6Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000414 in 1,206,294 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 3 hemizygotes in GnomAD. In-silico tool predicts 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: 0.0000178 AC: 2AN: 112410Hom.: 0 Cov.: 23 AF XY: 0.0000289 AC XY: 1AN XY: 34552
GnomAD3 exomes AF: 0.00000564 AC: 1AN: 177449Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 62297
GnomAD4 exome AF: 0.00000274 AC: 3AN: 1093884Hom.: 0 Cov.: 32 AF XY: 0.00000556 AC XY: 2AN XY: 359828
GnomAD4 genome AF: 0.0000178 AC: 2AN: 112410Hom.: 0 Cov.: 23 AF XY: 0.0000289 AC XY: 1AN XY: 34552
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.18G>T (p.K6N) alteration is located in exon 2 (coding exon 1) of the MAGEB2 gene. This alteration results from a G to T substitution at nucleotide position 18, causing the lysine (K) at amino acid position 6 to be replaced by an asparagine (N). 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