rs1009524
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_012301.4(MAGI2):āc.2784T>Cā(p.Asn928=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.101 in 1,607,866 control chromosomes in the GnomAD database, including 8,828 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Genomes: š 0.11 ( 983 hom., cov: 32)
Exomes š: 0.10 ( 7845 hom. )
Consequence
MAGI2
NM_012301.4 synonymous
NM_012301.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.772
Genes affected
MAGI2 (HGNC:18957): (membrane associated guanylate kinase, WW and PDZ domain containing 2) The protein encoded by this gene interacts with atrophin-1. Atrophin-1 contains a polyglutamine repeat, expansion of which is responsible for dentatorubral and pallidoluysian atrophy. This encoded protein is characterized by two WW domains, a guanylate kinase-like domain, and multiple PDZ domains. It has structural similarity to the membrane-associated guanylate kinase homologue (MAGUK) family. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.56).
BP6
?
Variant 7-78160086-A-G is Benign according to our data. Variant chr7-78160086-A-G is described in ClinVar as [Benign]. Clinvar id is 129563.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=-0.772 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.162 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MAGI2 | NM_012301.4 | c.2784T>C | p.Asn928= | synonymous_variant | 16/22 | ENST00000354212.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAGI2 | ENST00000354212.9 | c.2784T>C | p.Asn928= | synonymous_variant | 16/22 | 1 | NM_012301.4 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.112 AC: 16994AN: 152136Hom.: 982 Cov.: 32
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GnomAD3 exomes AF: 0.119 AC: 29574AN: 248480Hom.: 1917 AF XY: 0.115 AC XY: 15398AN XY: 134200
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GnomAD4 exome AF: 0.0999 AC: 145450AN: 1455612Hom.: 7845 Cov.: 31 AF XY: 0.0997 AC XY: 72070AN XY: 723206
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GnomAD4 genome ? AF: 0.112 AC: 17027AN: 152254Hom.: 983 Cov.: 32 AF XY: 0.114 AC XY: 8487AN XY: 74428
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ClinVar
Significance: Benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:3
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Apr 20, 2017 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Aug 20, 2019 | - - |
not specified Benign:1
Likely benign, no assertion criteria provided | clinical testing | Genetic Services Laboratory, University of Chicago | - | 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. - |
Computational scores
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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