7-78421278-T-C

Variant names:

• chr7-78421278-T-C
• rs2215379
• NM_012301.4:c.1046-52065A>G

Variant summary

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

The NM_012301.4(MAGI2):​c.1046-52065A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.722 in 152,054 control chromosomes in the GnomAD database, including 39,868 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 0.72 (39868 hom., cov: 32)
• Consequence: MAGI2 NM_012301.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.437
• Publications: 10 publications found

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]

MAGI2 Gene-Disease associations (from GenCC):

• nephrotic syndrome 15

  Inheritance: AR Classification: STRONG, LIMITED Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae)
• familial idiopathic steroid-resistant nephrotic syndrome

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• genetic developmental and epileptic encephalopathy

  Inheritance: AD Classification: LIMITED Submitted by: G2P
• epilepsy

  Inheritance: AD Classification: NO_KNOWN Submitted by: ClinGen

ENSG00000285892 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.772 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_012301.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAGI2	NM_012301.4	MANE Select	c.1046-52065A>G		intron	N/A	NP_036433.2
	MAGI2	NM_001301128.2		c.1046-52065A>G		intron	N/A	NP_001288057.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAGI2	ENST00000354212.9	TSL:1 MANE Select	c.1046-52065A>G		intron	N/A	ENSP00000346151.4
	MAGI2	ENST00000419488.5	TSL:1	c.1046-52065A>G		intron	N/A	ENSP00000405766.1
	MAGI2	ENST00000519748.5	TSL:1	c.-128-52065A>G		intron	N/A	ENSP00000486774.1

Frequencies

GnomAD3 genomes AF: 0.722 AC: 109634 AN: 151936 Hom.: 39839 Cov.: 32

Gnomad AFR AF: 0.780

Gnomad AMI AF: 0.585

Gnomad AMR AF: 0.754

Gnomad ASJ AF: 0.703

Gnomad EAS AF: 0.761

Gnomad SAS AF: 0.750

Gnomad FIN AF: 0.623

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.691

Gnomad OTH AF: 0.737

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

GnomAD4 genome AF: 0.722 AC: 109721 AN: 152054 Hom.: 39868 Cov.: 32 AF XY: 0.720 AC XY: 53518 AN XY: 74314

African (AFR) AF: 0.779 AC: 32343 AN: 41500

American (AMR) AF: 0.754 AC: 11521 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.703 AC: 2442 AN: 3472

East Asian (EAS) AF: 0.760 AC: 3912 AN: 5150

South Asian (SAS) AF: 0.751 AC: 3610 AN: 4808

European-Finnish (FIN) AF: 0.623 AC: 6577 AN: 10558

Middle Eastern (MID) AF: 0.782 AC: 230 AN: 294

European-Non Finnish (NFE) AF: 0.691 AC: 46991 AN: 67974

Other (OTH) AF: 0.741 AC: 1564 AN: 2112

Alfa AF: 0.702 Hom.: 65132

Bravo AF: 0.732

Asia WGS AF: 0.758 AC: 2637 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.4
DANN	Benign	0.83
PhyloP100		-0.44
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: rs2215379; hg19: chr7-78050595;