chrX-49166269-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_024859.4(MAGIX):c.875C>T(p.Pro292Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000109 in 1,194,708 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. 12/18 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 Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MAGIX | NM_024859.4 | c.875C>T | p.Pro292Leu | missense_variant | Exon 6 of 6 | ENST00000595224.6 | NP_079135.3 | |
MAGIX | NM_001395401.1 | c.698C>T | p.Pro233Leu | missense_variant | Exon 5 of 5 | NP_001382330.1 | ||
MAGIX | NM_001099681.2 | c.647C>T | p.Pro216Leu | missense_variant | Exon 5 of 5 | NP_001093151.2 | ||
MAGIX | NM_001099682.2 | c.632C>T | p.Pro211Leu | missense_variant | Exon 5 of 5 | NP_001093152.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000886 AC: 1AN: 112907Hom.: 0 Cov.: 24 AF XY: 0.00 AC XY: 0AN XY: 35057
GnomAD3 exomes AF: 0.00000688 AC: 1AN: 145401Hom.: 0 AF XY: 0.0000221 AC XY: 1AN XY: 45351
GnomAD4 exome AF: 0.0000111 AC: 12AN: 1081801Hom.: 0 Cov.: 30 AF XY: 0.0000256 AC XY: 9AN XY: 352221
GnomAD4 genome AF: 0.00000886 AC: 1AN: 112907Hom.: 0 Cov.: 24 AF XY: 0.00 AC XY: 0AN XY: 35057
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.875C>T (p.P292L) alteration is located in exon 6 (coding exon 6) of the MAGIX gene. This alteration results from a C to T substitution at nucleotide position 875, causing the proline (P) at amino acid position 292 to be replaced by a leucine (L). 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