3-65589685-A-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001033057.2(MAGI1):​c.430+32287T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.371 in 151,732 control chromosomes in the GnomAD database, including 11,841 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 0.37 ( 11841 hom., cov: 30)

Consequence

MAGI1
NM_001033057.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.30

Publications

3 publications found
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.02).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.642 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
MAGI1NM_001033057.2 linkc.430+32287T>G intron_variant Intron 2 of 22 ENST00000402939.7 NP_001028229.1 Q96QZ7-2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MAGI1ENST00000402939.7 linkc.430+32287T>G intron_variant Intron 2 of 22 1 NM_001033057.2 ENSP00000385450.2 Q96QZ7-2

Frequencies

GnomAD3 genomes
AF:
0.371
AC:
56286
AN:
151612
Hom.:
11837
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.176
Gnomad AMI
AF:
0.363
Gnomad AMR
AF:
0.391
Gnomad ASJ
AF:
0.378
Gnomad EAS
AF:
0.661
Gnomad SAS
AF:
0.420
Gnomad FIN
AF:
0.540
Gnomad MID
AF:
0.304
Gnomad NFE
AF:
0.435
Gnomad OTH
AF:
0.347
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.371
AC:
56316
AN:
151732
Hom.:
11841
Cov.:
30
AF XY:
0.378
AC XY:
28012
AN XY:
74128
show subpopulations
African (AFR)
AF:
0.176
AC:
7294
AN:
41390
American (AMR)
AF:
0.392
AC:
5976
AN:
15264
Ashkenazi Jewish (ASJ)
AF:
0.378
AC:
1311
AN:
3468
East Asian (EAS)
AF:
0.661
AC:
3387
AN:
5124
South Asian (SAS)
AF:
0.418
AC:
2005
AN:
4794
European-Finnish (FIN)
AF:
0.540
AC:
5677
AN:
10520
Middle Eastern (MID)
AF:
0.318
AC:
93
AN:
292
European-Non Finnish (NFE)
AF:
0.435
AC:
29513
AN:
67866
Other (OTH)
AF:
0.347
AC:
730
AN:
2106
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.505
Heterozygous variant carriers
0
1639
3278
4917
6556
8195
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
548
1096
1644
2192
2740
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.296
Hom.:
985
Bravo
AF:
0.352
Asia WGS
AF:
0.483
AC:
1678
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.0040
DANN
Benign
0.60
PhyloP100
-3.3
Mutation Taster
=100/0
polymorphism (auto)

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs12635482; hg19: chr3-65575360; API