rs884067

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001033057.2(MAGI1):​c.314-44999C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.315 in 152,054 control chromosomes in the GnomAD database, including 7,737 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 0.32 ( 7737 hom., cov: 33)

Consequence

MAGI1
NM_001033057.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.12
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 made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.348 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
MAGI1NM_001033057.2 linkuse as main transcriptc.314-44999C>T intron_variant ENST00000402939.7 NP_001028229.1 Q96QZ7-2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
MAGI1ENST00000402939.7 linkuse as main transcriptc.314-44999C>T intron_variant 1 NM_001033057.2 ENSP00000385450.2 Q96QZ7-2

Frequencies

GnomAD3 genomes
AF:
0.315
AC:
47889
AN:
151936
Hom.:
7724
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.276
Gnomad AMI
AF:
0.313
Gnomad AMR
AF:
0.274
Gnomad ASJ
AF:
0.218
Gnomad EAS
AF:
0.348
Gnomad SAS
AF:
0.274
Gnomad FIN
AF:
0.331
Gnomad MID
AF:
0.215
Gnomad NFE
AF:
0.352
Gnomad OTH
AF:
0.303
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.315
AC:
47929
AN:
152054
Hom.:
7737
Cov.:
33
AF XY:
0.310
AC XY:
23066
AN XY:
74322
show subpopulations
Gnomad4 AFR
AF:
0.276
Gnomad4 AMR
AF:
0.274
Gnomad4 ASJ
AF:
0.218
Gnomad4 EAS
AF:
0.347
Gnomad4 SAS
AF:
0.275
Gnomad4 FIN
AF:
0.331
Gnomad4 NFE
AF:
0.352
Gnomad4 OTH
AF:
0.306
Alfa
AF:
0.337
Hom.:
11894
Bravo
AF:
0.311
Asia WGS
AF:
0.349
AC:
1214
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
0.26
DANN
Benign
0.71

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs884067; hg19: chr3-65652762; API