X-141905831-A-C
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_005462.5(MAGEC1):āc.427A>Cā(p.Ile143Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000341 in 1,203,325 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 14 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_005462.5 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/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MAGEC1 | NM_005462.5 | c.427A>C | p.Ile143Leu | missense_variant | 4/4 | ENST00000285879.5 | NP_005453.2 | |
MAGEC1 | XM_011531418.3 | c.427A>C | p.Ile143Leu | missense_variant | 4/4 | XP_011529720.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MAGEC1 | ENST00000285879.5 | c.427A>C | p.Ile143Leu | missense_variant | 4/4 | 1 | NM_005462.5 | ENSP00000285879 | P3 | |
MAGEC1 | ENST00000406005.2 | c.-115+284A>C | intron_variant | 1 | ENSP00000385500 | A2 |
Frequencies
GnomAD3 genomes AF: 0.0000718 AC: 8AN: 111386Hom.: 0 Cov.: 24 AF XY: 0.0000882 AC XY: 3AN XY: 34014
GnomAD3 exomes AF: 0.0000497 AC: 9AN: 181139Hom.: 0 AF XY: 0.0000448 AC XY: 3AN XY: 66955
GnomAD4 exome AF: 0.0000302 AC: 33AN: 1091939Hom.: 0 Cov.: 36 AF XY: 0.0000303 AC XY: 11AN XY: 363265
GnomAD4 genome AF: 0.0000718 AC: 8AN: 111386Hom.: 0 Cov.: 24 AF XY: 0.0000882 AC XY: 3AN XY: 34014
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 14, 2023 | The c.427A>C (p.I143L) alteration is located in exon 4 (coding exon 2) of the MAGEC1 gene. This alteration results from a A to C substitution at nucleotide position 427, causing the isoleucine (I) at amino acid position 143 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