chrX-49163818-C-G
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_024859.4(MAGIX):c.85C>G(p.Arg29Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000191 in 1,047,863 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 6 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_024859.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MAGIX | NM_024859.4 | c.85C>G | p.Arg29Gly | missense_variant | Exon 2 of 6 | ENST00000595224.6 | NP_079135.3 | |
MAGIX | NM_001099681.2 | c.85C>G | p.Arg29Gly | missense_variant | Exon 2 of 5 | NP_001093151.2 | ||
MAGIX | NM_001099682.2 | c.85C>G | p.Arg29Gly | missense_variant | Exon 2 of 5 | NP_001093152.2 | ||
MAGIX | NM_001395401.1 | c.-166C>G | 5_prime_UTR_variant | Exon 2 of 5 | NP_001382330.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000621 AC: 7AN: 112632Hom.: 0 Cov.: 23 AF XY: 0.0000573 AC XY: 2AN XY: 34890
GnomAD4 exome AF: 0.0000139 AC: 13AN: 935231Hom.: 0 Cov.: 29 AF XY: 0.0000136 AC XY: 4AN XY: 294349
GnomAD4 genome AF: 0.0000621 AC: 7AN: 112632Hom.: 0 Cov.: 23 AF XY: 0.0000573 AC XY: 2AN XY: 34890
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.85C>G (p.R29G) alteration is located in exon 2 (coding exon 2) of the MAGIX gene. This alteration results from a C to G substitution at nucleotide position 85, causing the arginine (R) at amino acid position 29 to be replaced by a glycine (G). 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