chr3-65361249-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_001033057.2(MAGI1):c.3584G>A(p.Arg1195His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000102 in 1,613,996 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: 0.000112 AC: 17AN: 152172Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000123 AC: 31AN: 251322Hom.: 0 AF XY: 0.000110 AC XY: 15AN XY: 135868
GnomAD4 exome AF: 0.000101 AC: 147AN: 1461824Hom.: 0 Cov.: 33 AF XY: 0.0000908 AC XY: 66AN XY: 727216
GnomAD4 genome AF: 0.000112 AC: 17AN: 152172Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74348
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.3584G>A (p.R1195H) 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 3584, causing the arginine (R) at amino acid position 1195 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