chrX-49164764-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_024859.4(MAGIX):c.254C>T(p.Ala85Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000173 in 1,210,417 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 7 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/20 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.254C>T | p.Ala85Val | missense_variant | Exon 3 of 6 | ENST00000595224.6 | NP_079135.3 | |
MAGIX | NM_001395401.1 | c.4C>T | p.Pro2Ser | missense_variant | Exon 3 of 5 | NP_001382330.1 | ||
MAGIX | NM_001099681.2 | c.254C>T | p.Ala85Val | missense_variant | Exon 3 of 5 | NP_001093151.2 | ||
MAGIX | NM_001099682.2 | c.254C>T | p.Ala85Val | missense_variant | Exon 3 of 5 | NP_001093152.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000799 AC: 9AN: 112572Hom.: 0 Cov.: 24 AF XY: 0.0000864 AC XY: 3AN XY: 34740
GnomAD3 exomes AF: 0.0000442 AC: 8AN: 180955Hom.: 0 AF XY: 0.0000446 AC XY: 3AN XY: 67239
GnomAD4 exome AF: 0.0000109 AC: 12AN: 1097845Hom.: 0 Cov.: 30 AF XY: 0.0000110 AC XY: 4AN XY: 363271
GnomAD4 genome AF: 0.0000799 AC: 9AN: 112572Hom.: 0 Cov.: 24 AF XY: 0.0000864 AC XY: 3AN XY: 34740
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.254C>T (p.A85V) alteration is located in exon 3 (coding exon 3) of the MAGIX gene. This alteration results from a C to T substitution at nucleotide position 254, causing the alanine (A) at amino acid position 85 to be replaced by a valine (V). 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