rs1016553

Positions:

• chr3-65393619-A-G
• chr3-65393619-A-T

Variant summary

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

The NM_001033057.2(MAGI1):​c.2200-2261T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.877 in 152,172 control chromosomes in the GnomAD database, including 59,147 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 0.88 (59147 hom., cov: 31)
• Consequence: MAGI1 NM_001033057.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.239

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.947 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAGI1	NM_001033057.2	c.2200-2261T>C		intron_variant		ENST00000402939.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAGI1	ENST00000402939.7	c.2200-2261T>C		intron_variant		1	NM_001033057.2	A2

Frequencies

GnomAD3 genomes AF: 0.877 AC: 133357 AN: 152054 Hom.: 59138 Cov.: 31

Gnomad AFR AF: 0.790

Gnomad AMI AF: 0.901

Gnomad AMR AF: 0.801

Gnomad ASJ AF: 0.981

Gnomad EAS AF: 0.678

Gnomad SAS AF: 0.766

Gnomad FIN AF: 0.942

Gnomad MID AF: 0.962

Gnomad NFE AF: 0.953

Gnomad OTH AF: 0.906

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

GnomAD4 genome AF: 0.877 AC: 133409 AN: 152172 Hom.: 59147 Cov.: 31 AF XY: 0.871 AC XY: 64772 AN XY: 74396

Gnomad4 AFR AF: 0.790

Gnomad4 AMR AF: 0.800

Gnomad4 ASJ AF: 0.981

Gnomad4 EAS AF: 0.678

Gnomad4 SAS AF: 0.765

Gnomad4 FIN AF: 0.942

Gnomad4 NFE AF: 0.953

Gnomad4 OTH AF: 0.903

Alfa AF: 0.932 Hom.: 94897

Bravo AF: 0.864

Asia WGS AF: 0.698 AC: 2431 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.4
DANN	Benign	0.69

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: rs1016553; hg19: chr3-65379294;