chrX-54810017-A-G
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_177433.3(MAGED2):āc.341A>Gā(p.Gln114Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000151 in 1,205,111 control chromosomes in the GnomAD database, including 1 homozygotes. There are 70 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Consequence
NM_177433.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MAGED2 | NM_177433.3 | c.341A>G | p.Gln114Arg | missense_variant | 3/13 | ENST00000375068.6 | |
MAGED2 | NM_014599.6 | c.341A>G | p.Gln114Arg | missense_variant | 3/13 | ||
MAGED2 | NM_201222.3 | c.341A>G | p.Gln114Arg | missense_variant | 3/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAGED2 | ENST00000375068.6 | c.341A>G | p.Gln114Arg | missense_variant | 3/13 | 1 | NM_177433.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000632 AC: 7AN: 110753Hom.: 0 Cov.: 21 AF XY: 0.0000911 AC XY: 3AN XY: 32931
GnomAD3 exomes AF: 0.000110 AC: 19AN: 172511Hom.: 0 AF XY: 0.000120 AC XY: 7AN XY: 58483
GnomAD4 exome AF: 0.000160 AC: 175AN: 1094306Hom.: 1 Cov.: 34 AF XY: 0.000186 AC XY: 67AN XY: 360240
GnomAD4 genome AF: 0.0000632 AC: 7AN: 110805Hom.: 0 Cov.: 21 AF XY: 0.0000909 AC XY: 3AN XY: 32993
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Aug 17, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at