rs1230661
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001142782.2(MAGI3):c.1966+452A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.806 in 152,232 control chromosomes in the GnomAD database, including 50,600 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.81 ( 50600 hom., cov: 34)
Consequence
MAGI3
NM_001142782.2 intron
NM_001142782.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0120
Genes affected
MAGI3 (HGNC:29647): (membrane associated guanylate kinase, WW and PDZ domain containing 3) Predicted to enable frizzled binding activity. Predicted to be involved in signal transduction. Predicted to act upstream of or within positive regulation of JUN kinase activity. Located in cell junction. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.948 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MAGI3 | NM_001142782.2 | c.1966+452A>G | intron_variant | ENST00000307546.14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAGI3 | ENST00000307546.14 | c.1966+452A>G | intron_variant | 5 | NM_001142782.2 | ||||
MAGI3 | ENST00000369611.4 | c.1966+452A>G | intron_variant | 1 | P1 | ||||
MAGI3 | ENST00000369617.8 | c.2041+452A>G | intron_variant | 1 | |||||
MAGI3 | ENST00000369615.5 | c.1966+452A>G | intron_variant | 5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.806 AC: 122648AN: 152114Hom.: 50540 Cov.: 34
GnomAD3 genomes
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34
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.806 AC: 122767AN: 152232Hom.: 50600 Cov.: 34 AF XY: 0.801 AC XY: 59589AN XY: 74418
GnomAD4 genome
?
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34
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59589
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74418
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2282
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at