X-49166248-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.854C>G(p.Pro285Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000833 in 1,200,812 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 2 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 11/18 in silico tools predict 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.854C>G | p.Pro285Arg | missense_variant | Exon 6 of 6 | ENST00000595224.6 | NP_079135.3 | |
MAGIX | NM_001395401.1 | c.677C>G | p.Pro226Arg | missense_variant | Exon 5 of 5 | NP_001382330.1 | ||
MAGIX | NM_001099681.2 | c.626C>G | p.Pro209Arg | missense_variant | Exon 5 of 5 | NP_001093151.2 | ||
MAGIX | NM_001099682.2 | c.611C>G | p.Pro204Arg | missense_variant | Exon 5 of 5 | NP_001093152.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000886 AC: 1AN: 112815Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34957
GnomAD4 exome AF: 0.00000735 AC: 8AN: 1087945Hom.: 0 Cov.: 31 AF XY: 0.00000563 AC XY: 2AN XY: 355555
GnomAD4 genome AF: 0.0000177 AC: 2AN: 112867Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 35019
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.854C>G (p.P285R) alteration is located in exon 6 (coding exon 6) of the MAGIX gene. This alteration results from a C to G substitution at nucleotide position 854, causing the proline (P) at amino acid position 285 to be replaced by an arginine (R). 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