3-65825239-T-G

Position:

• chr3-65825239-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001033057.2(MAGI1):​c.314-203151A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.52 in 152,094 control chromosomes in the GnomAD database, including 21,118 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 0.52 (21118 hom., cov: 33)
• Consequence: MAGI1 NM_001033057.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.699

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]

MAGI1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.738 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAGI1	NM_001033057.2	c.314-203151A>C		intron_variant		ENST00000402939.7	NP_001028229.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAGI1	ENST00000402939.7	c.314-203151A>C		intron_variant		1	NM_001033057.2	ENSP00000385450.2

Frequencies

GnomAD3 genomes AF: 0.520 AC: 79067 AN: 151976 Hom.: 21122 Cov.: 33

Gnomad AFR AF: 0.422

Gnomad AMI AF: 0.561

Gnomad AMR AF: 0.587

Gnomad ASJ AF: 0.491

Gnomad EAS AF: 0.757

Gnomad SAS AF: 0.531

Gnomad FIN AF: 0.609

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.534

Gnomad OTH AF: 0.514

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

GnomAD4 genome AF: 0.520 AC: 79097 AN: 152094 Hom.: 21118 Cov.: 33 AF XY: 0.525 AC XY: 39043 AN XY: 74358

Gnomad4 AFR AF: 0.421

Gnomad4 AMR AF: 0.587

Gnomad4 ASJ AF: 0.491

Gnomad4 EAS AF: 0.757

Gnomad4 SAS AF: 0.531

Gnomad4 FIN AF: 0.609

Gnomad4 NFE AF: 0.534

Gnomad4 OTH AF: 0.511

Alfa AF: 0.512 Hom.: 2699

Bravo AF: 0.519

Asia WGS AF: 0.632 AC: 2201 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	0.38
DANN	Benign	0.74

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

Other links and lift over

dbSNP: rs1495448; hg19: chr3-65810914;