X-142203431-C-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_016249.4(MAGEC2):c.557G>T(p.Arg186Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000405 in 1,209,558 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 16 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R186C) has been classified as Uncertain significance.
Frequency
Consequence
NM_016249.4 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: 0.0000269 AC: 3AN: 111662Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33850
GnomAD3 exomes AF: 0.0000382 AC: 7AN: 183339Hom.: 0 AF XY: 0.0000590 AC XY: 4AN XY: 67787
GnomAD4 exome AF: 0.0000419 AC: 46AN: 1097896Hom.: 0 Cov.: 33 AF XY: 0.0000440 AC XY: 16AN XY: 363258
GnomAD4 genome AF: 0.0000269 AC: 3AN: 111662Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33850
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.557G>T (p.R186L) alteration is located in exon 3 (coding exon 1) of the MAGEC2 gene. This alteration results from a G to T substitution at nucleotide position 557, causing the arginine (R) at amino acid position 186 to be replaced by a leucine (L). 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