X-76427968-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_020932.3(MAGEE1):c.38G>A(p.Arg13His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000166 in 1,202,359 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples 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 (★).
Frequency
Consequence
NM_020932.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MAGEE1 | NM_020932.3 | c.38G>A | p.Arg13His | missense_variant | 1/1 | ENST00000361470.4 | NP_065983.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MAGEE1 | ENST00000361470.4 | c.38G>A | p.Arg13His | missense_variant | 1/1 | NM_020932.3 | ENSP00000354912 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000886 AC: 1AN: 112848Hom.: 0 Cov.: 26 AF XY: 0.00 AC XY: 0AN XY: 35010
GnomAD4 exome AF: 9.18e-7 AC: 1AN: 1089511Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 356923
GnomAD4 genome AF: 0.00000886 AC: 1AN: 112848Hom.: 0 Cov.: 26 AF XY: 0.00 AC XY: 0AN XY: 35010
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 18, 2021 | The c.38G>A (p.R13H) alteration is located in exon 1 (coding exon 1) of the MAGEE1 gene. This alteration results from a G to A substitution at nucleotide position 38, causing the arginine (R) at amino acid position 13 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