X-51894745-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001005333.2(MAGED1):c.164C>T(p.Pro55Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000164 in 1,155,464 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 6 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 11/17 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 -6 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000277 AC: 3AN: 108130Hom.: 0 Cov.: 20 AF XY: 0.00 AC XY: 0AN XY: 30486
GnomAD3 exomes AF: 0.0000226 AC: 3AN: 132918Hom.: 0 AF XY: 0.0000231 AC XY: 1AN XY: 43282
GnomAD4 exome AF: 0.0000153 AC: 16AN: 1047290Hom.: 0 Cov.: 32 AF XY: 0.0000177 AC XY: 6AN XY: 339552
GnomAD4 genome AF: 0.0000277 AC: 3AN: 108174Hom.: 0 Cov.: 20 AF XY: 0.00 AC XY: 0AN XY: 30540
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 24, 2024 | The c.164C>T (p.P55L) 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 164, causing the proline (P) at amino acid position 55 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