X-77856754-A-T
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_001367916.1(MAGT1):c.651T>A(p.Thr217Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00285 in 1,207,966 control chromosomes in the GnomAD database, including 51 homozygotes. There are 889 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001367916.1 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MAGT1 | NM_001367916.1 | c.651T>A | p.Thr217Thr | synonymous_variant | Exon 5 of 10 | ENST00000618282.5 | NP_001354845.1 | |
MAGT1 | NM_032121.5 | c.747T>A | p.Thr249Thr | synonymous_variant | Exon 5 of 10 | NP_115497.4 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0150 AC: 1676AN: 111837Hom.: 27 Cov.: 23 AF XY: 0.0126 AC XY: 429AN XY: 34027
GnomAD3 exomes AF: 0.00449 AC: 820AN: 182455Hom.: 12 AF XY: 0.00268 AC XY: 180AN XY: 67165
GnomAD4 exome AF: 0.00161 AC: 1770AN: 1096075Hom.: 24 Cov.: 28 AF XY: 0.00127 AC XY: 459AN XY: 361585
GnomAD4 genome AF: 0.0150 AC: 1678AN: 111891Hom.: 27 Cov.: 23 AF XY: 0.0126 AC XY: 430AN XY: 34091
ClinVar
Submissions by phenotype
not provided Benign:2
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not specified Benign:1
Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed. -
X-linked immunodeficiency with magnesium defect, Epstein-Barr virus infection and neoplasia Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at