X-49165298-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_024859.4(MAGIX):c.616C>T(p.Arg206Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000254 in 1,180,852 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 9 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 12/20 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. R206H) has been classified 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 -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MAGIX | NM_024859.4 | c.616C>T | p.Arg206Cys | missense_variant | Exon 5 of 6 | ENST00000595224.6 | NP_079135.3 | |
MAGIX | NM_001395401.1 | c.439C>T | p.Arg147Cys | missense_variant | Exon 4 of 5 | NP_001382330.1 | ||
MAGIX | NM_001099681.2 | c.388C>T | p.Arg130Cys | missense_variant | Exon 4 of 5 | NP_001093151.2 | ||
MAGIX | NM_001099682.2 | c.388C>T | p.Arg130Cys | missense_variant | Exon 4 of 5 | NP_001093152.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000802 AC: 9AN: 112288Hom.: 0 Cov.: 24 AF XY: 0.000116 AC XY: 4AN XY: 34460
GnomAD3 exomes AF: 0.00000763 AC: 1AN: 131041Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 40197
GnomAD4 exome AF: 0.0000197 AC: 21AN: 1068564Hom.: 0 Cov.: 31 AF XY: 0.0000144 AC XY: 5AN XY: 346594
GnomAD4 genome AF: 0.0000802 AC: 9AN: 112288Hom.: 0 Cov.: 24 AF XY: 0.000116 AC XY: 4AN XY: 34460
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.616C>T (p.R206C) alteration is located in exon 5 (coding exon 5) of the MAGIX gene. This alteration results from a C to T substitution at nucleotide position 616, causing the arginine (R) at amino acid position 206 to be replaced by a cysteine (C). 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