rs7812015

chr7-78127407-C-T

Variant summary

Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_Moderate BP6_Very_Strong BP7 BA1

The NM_012301.4(MAGI2):c.3213G>A(p.Ser1071=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.857 in 1,601,268 control chromosomes in the GnomAD database, including 591,156 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.86 (56215 hom., cov: 30)
  • Exomes 𝑓: 0.86 (534941 hom.)
• Consequence: MAGI2 NM_012301.4 synonymous
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:5
• Conservation: PhyloP100: 0.549

Genes affected

MAGI2 (HGNC:18957): (membrane associated guanylate kinase, WW and PDZ domain containing 2) The protein encoded by this gene interacts with atrophin-1. Atrophin-1 contains a polyglutamine repeat, expansion of which is responsible for dentatorubral and pallidoluysian atrophy. This encoded protein is characterized by two WW domains, a guanylate kinase-like domain, and multiple PDZ domains. It has structural similarity to the membrane-associated guanylate kinase homologue (MAGUK) family. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -19 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.34).
• BP6: Variant 7-78127407-C-T is Benign according to our data. Variant chr7-78127407-C-T is described in ClinVar as [Benign]. Clinvar id is 129564.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BP7: Synonymous conserved (PhyloP=0.549 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.901 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAGI2	NM_012301.4	c.3213G>A	p.Ser1071=	synonymous_variant	19/22	ENST00000354212.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAGI2	ENST00000354212.9	c.3213G>A	p.Ser1071=	synonymous_variant	19/22	1	NM_012301.4	P4

Frequencies

GnomAD3 genomes AF: 0.857 AC: 130215 AN: 152000 Hom.: 56167 Cov.: 30

Gnomad AFR AF: 0.908

Gnomad AMI AF: 0.693

Gnomad AMR AF: 0.768

Gnomad ASJ AF: 0.795

Gnomad EAS AF: 0.589

Gnomad SAS AF: 0.765

Gnomad FIN AF: 0.870

Gnomad MID AF: 0.801

Gnomad NFE AF: 0.876

Gnomad OTH AF: 0.845

GnomAD3 exomes AF: 0.813 AC: 196853 AN: 241984 Hom.: 81326 AF XY: 0.816 AC XY: 107180 AN XY: 131376

Gnomad AFR exome AF: 0.911

Gnomad AMR exome AF: 0.697

Gnomad ASJ exome AF: 0.792

Gnomad EAS exome AF: 0.579

Gnomad SAS exome AF: 0.776

Gnomad FIN exome AF: 0.872

Gnomad NFE exome AF: 0.877

Gnomad OTH exome AF: 0.827

GnomAD4 exome AF: 0.857 AC: 1241572 AN: 1449150 Hom.: 534941 Cov.: 37 AF XY: 0.854 AC XY: 616274 AN XY: 721334

Gnomad4 AFR exome AF: 0.913

Gnomad4 AMR exome AF: 0.707

Gnomad4 ASJ exome AF: 0.802

Gnomad4 EAS exome AF: 0.594

Gnomad4 SAS exome AF: 0.770

Gnomad4 FIN exome AF: 0.879

Gnomad4 NFE exome AF: 0.879

Gnomad4 OTH exome AF: 0.844

GnomAD4 genome AF: 0.857 AC: 130321 AN: 152118 Hom.: 56215 Cov.: 30 AF XY: 0.849 AC XY: 63102 AN XY: 74368

Gnomad4 AFR AF: 0.908

Gnomad4 AMR AF: 0.768

Gnomad4 ASJ AF: 0.795

Gnomad4 EAS AF: 0.589

Gnomad4 SAS AF: 0.764

Gnomad4 FIN AF: 0.870

Gnomad4 NFE AF: 0.876

Gnomad4 OTH AF: 0.846

Alfa AF: 0.857 Hom.: 58564

Bravo AF: 0.850

Asia WGS AF: 0.730 AC: 2542 AN: 3478

EpiCase AF: 0.858

EpiControl AF: 0.860

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:3

Benign, criteria provided, single submitter	clinical testing	Invitae	Jan 31, 2024	- -
Benign, criteria provided, single submitter	clinical testing	Athena Diagnostics	Apr 20, 2017	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Aug 20, 2019	- -

not specified Benign:1

Likely benign, no assertion criteria provided

clinical testing

Genetic Services Laboratory, University of Chicago

-

Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed. -

Nephrotic syndrome 15 Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Sep 05, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.34
Cadd	Benign	5.6
Dann	Benign	0.61

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: rs7812015; hg19: chr7-77756724; COSMIC: COSV62650317;