X-54809804-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_177433.3(MAGED2):c.128C>T(p.Pro43Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000483 in 1,201,746 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. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_177433.3 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 | UniProt |
---|---|---|---|---|---|---|---|
MAGED2 | NM_177433.3 | c.128C>T | p.Pro43Leu | missense_variant | 3/13 | ENST00000375068.6 | |
MAGED2 | NM_014599.6 | c.128C>T | p.Pro43Leu | missense_variant | 3/13 | ||
MAGED2 | NM_201222.3 | c.128C>T | p.Pro43Leu | missense_variant | 3/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAGED2 | ENST00000375068.6 | c.128C>T | p.Pro43Leu | missense_variant | 3/13 | 1 | NM_177433.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000244 AC: 27AN: 110746Hom.: 0 Cov.: 22 AF XY: 0.000152 AC XY: 5AN XY: 32976
GnomAD3 exomes AF: 0.0000843 AC: 14AN: 166019Hom.: 0 AF XY: 0.0000561 AC XY: 3AN XY: 53499
GnomAD4 exome AF: 0.0000284 AC: 31AN: 1090945Hom.: 0 Cov.: 31 AF XY: 0.0000252 AC XY: 9AN XY: 357341
GnomAD4 genome ? AF: 0.000244 AC: 27AN: 110801Hom.: 0 Cov.: 22 AF XY: 0.000151 AC XY: 5AN XY: 33041
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 21, 2023 | The c.128C>T (p.P43L) alteration is located in exon 3 (coding exon 2) of the MAGED2 gene. This alteration results from a C to T substitution at nucleotide position 128, causing the proline (P) at amino acid position 43 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