chrX-51894771-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_001005333.2(MAGED1):c.190C>T(p.Pro64Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000875 in 1,142,624 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 2 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 12/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001005333.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000184 AC: 2AN: 108895Hom.: 0 Cov.: 20 AF XY: 0.0000321 AC XY: 1AN XY: 31185
GnomAD3 exomes AF: 0.00000777 AC: 1AN: 128653Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 43285
GnomAD4 exome AF: 0.00000774 AC: 8AN: 1033729Hom.: 0 Cov.: 32 AF XY: 0.00000301 AC XY: 1AN XY: 332733
GnomAD4 genome AF: 0.0000184 AC: 2AN: 108895Hom.: 0 Cov.: 20 AF XY: 0.0000321 AC XY: 1AN XY: 31185
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.190C>T (p.P64S) alteration is located in exon 3 (coding exon 2) of the MAGED1 gene. This alteration results from a C to T substitution at nucleotide position 190, causing the proline (P) at amino acid position 64 to be replaced by a serine (S). 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