3-65361240-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_001033057.2(MAGI1):c.3593G>A(p.Arg1198His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000204 in 1,614,164 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001033057.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152202Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251390Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135884
GnomAD4 exome AF: 0.0000192 AC: 28AN: 1461844Hom.: 0 Cov.: 33 AF XY: 0.0000138 AC XY: 10AN XY: 727226
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152320Hom.: 0 Cov.: 32 AF XY: 0.0000537 AC XY: 4AN XY: 74494
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.3593G>A (p.R1198H) alteration is located in exon 22 (coding exon 22) of the MAGI1 gene. This alteration results from a G to A substitution at nucleotide position 3593, causing the arginine (R) at amino acid position 1198 to be replaced by a histidine (H). 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