3-65381897-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_001033057.2(MAGI1):c.2681G>A(p.Arg894Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000198 in 1,612,928 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 -4 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152124Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000320 AC: 8AN: 249642Hom.: 0 AF XY: 0.0000444 AC XY: 6AN XY: 135018
GnomAD4 exome AF: 0.0000199 AC: 29AN: 1460804Hom.: 0 Cov.: 30 AF XY: 0.0000179 AC XY: 13AN XY: 726688
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152124Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74306
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2681G>A (p.R894Q) alteration is located in exon 16 (coding exon 16) of the MAGI1 gene. This alteration results from a G to A substitution at nucleotide position 2681, causing the arginine (R) at amino acid position 894 to be replaced by a glutamine (Q). 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