X-49165328-C-G
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_024859.4(MAGIX):c.646C>G(p.Pro216Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000139 in 1,176,518 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 60 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 14/20 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.646C>G | p.Pro216Ala | missense_variant | Exon 5 of 6 | ENST00000595224.6 | NP_079135.3 | |
MAGIX | NM_001395401.1 | c.469C>G | p.Pro157Ala | missense_variant | Exon 4 of 5 | NP_001382330.1 | ||
MAGIX | NM_001099681.2 | c.418C>G | p.Pro140Ala | missense_variant | Exon 4 of 5 | NP_001093151.2 | ||
MAGIX | NM_001099682.2 | c.418C>G | p.Pro140Ala | missense_variant | Exon 4 of 5 | NP_001093152.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000170 AC: 19AN: 111799Hom.: 0 Cov.: 23 AF XY: 0.000147 AC XY: 5AN XY: 33971
GnomAD3 exomes AF: 0.000122 AC: 16AN: 131462Hom.: 0 AF XY: 0.0000561 AC XY: 2AN XY: 35672
GnomAD4 exome AF: 0.000135 AC: 144AN: 1064719Hom.: 0 Cov.: 31 AF XY: 0.000161 AC XY: 55AN XY: 340659
GnomAD4 genome AF: 0.000170 AC: 19AN: 111799Hom.: 0 Cov.: 23 AF XY: 0.000147 AC XY: 5AN XY: 33971
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.646C>G (p.P216A) alteration is located in exon 5 (coding exon 5) of the MAGIX gene. This alteration results from a C to G substitution at nucleotide position 646, causing the proline (P) at amino acid position 216 to be replaced by an alanine (A). 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