chr3-65712479-C-A

Variant names:

• chr3-65712479-C-A
• rs2372184
• NM_001033057.2:c.314-90391G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001033057.2(MAGI1):​c.314-90391G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.375 in 148,526 control chromosomes in the GnomAD database, including 10,789 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 0.38 (10789 hom., cov: 28)
• Consequence: MAGI1 NM_001033057.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.511
• Publications: 2 publications found

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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.414 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAGI1	NM_001033057.2	c.314-90391G>T		intron_variant	Intron 1 of 22	ENST00000402939.7	NP_001028229.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAGI1	ENST00000402939.7	c.314-90391G>T		intron_variant	Intron 1 of 22	1	NM_001033057.2	ENSP00000385450.2

Frequencies

GnomAD3 genomes AF: 0.375 AC: 55687 AN: 148472 Hom.: 10787 Cov.: 28

Gnomad AFR AF: 0.361

Gnomad AMI AF: 0.344

Gnomad AMR AF: 0.312

Gnomad ASJ AF: 0.330

Gnomad EAS AF: 0.300

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.397

Gnomad MID AF: 0.245

Gnomad NFE AF: 0.418

Gnomad OTH AF: 0.377

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.375 AC: 55708 AN: 148526 Hom.: 10789 Cov.: 28 AF XY: 0.366 AC XY: 26456 AN XY: 72242

African (AFR) AF: 0.361 AC: 14539 AN: 40330

American (AMR) AF: 0.312 AC: 4665 AN: 14962

Ashkenazi Jewish (ASJ) AF: 0.330 AC: 1141 AN: 3454

East Asian (EAS) AF: 0.301 AC: 1523 AN: 5060

South Asian (SAS) AF: 0.163 AC: 768 AN: 4720

European-Finnish (FIN) AF: 0.397 AC: 3725 AN: 9386

Middle Eastern (MID) AF: 0.250 AC: 71 AN: 284

European-Non Finnish (NFE) AF: 0.418 AC: 28182 AN: 67362

Other (OTH) AF: 0.379 AC: 782 AN: 2062

Alfa AF: 0.160 Hom.: 229

Bravo AF: 0.382

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.28
PhyloP100		0.51
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

Other links and lift over

dbSNP: rs2372184; hg19: chr3-65698154;