3-65364892-G-T
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Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001033057.2(MAGI1):c.3251C>A(p.Thr1084Asn) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.0 ( 0 hom., cov: 32)
Failed GnomAD Quality Control
Consequence
MAGI1
NM_001033057.2 missense
NM_001033057.2 missense
Scores
1
5
11
Clinical Significance
Conservation
PhyloP100: 6.75
Genes affected
MAGI1 (HGNC:946): (membrane associated guanylate kinase, WW and PDZ domain containing 1) The protein encoded by this gene is a member of the membrane-associated guanylate kinase homologue (MAGUK) family. MAGUK proteins participate in the assembly of multiprotein complexes on the inner surface of the plasma membrane at regions of cell-cell contact. The product of this gene may play a role as scaffolding protein at cell-cell junctions. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.31192017).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MAGI1 | NM_001033057.2 | c.3251C>A | p.Thr1084Asn | missense_variant | 19/23 | ENST00000402939.7 | NP_001028229.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MAGI1 | ENST00000402939.7 | c.3251C>A | p.Thr1084Asn | missense_variant | 19/23 | 1 | NM_001033057.2 | ENSP00000385450 | A2 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 0AN: 152102Hom.: 0 Cov.: 32 FAILED QC
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GnomAD4 exome Cov.: 31
GnomAD4 exome
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31
GnomAD4 genome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 152102Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74292
GnomAD4 genome
Data not reliable, filtered out with message: AC0
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74292
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 13, 2022 | The c.3251C>A (p.T1084N) alteration is located in exon 19 (coding exon 19) of the MAGI1 gene. This alteration results from a C to A substitution at nucleotide position 3251, causing the threonine (T) at amino acid position 1084 to be replaced by an asparagine (N). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
.;.;T;.;.;.;.;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
M_CAP
Benign
D
MetaRNN
Benign
T;T;T;T;T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
.;.;.;.;.;M;.;.
MutationTaster
Benign
D;D;D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;.;.;N;N;N;N;N
REVEL
Benign
Sift
Benign
T;.;.;D;T;T;T;T
Sift4G
Benign
T;T;T;T;T;T;T;T
Polyphen
P;.;.;P;.;D;P;.
Vest4
MutPred
Loss of glycosylation at T1112 (P = 0.0028);.;.;.;.;.;.;.;
MVP
MPC
1.5
ClinPred
D
GERP RS
gMVP
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