NM_012301.4:c.1045+10775T>C

Variant names:

• chr7-78478986-A-G
• rs6951193
• NM_012301.4:c.1045+10775T>C

Variant summary

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

The NM_012301.4(MAGI2):​c.1045+10775T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.304 in 151,764 control chromosomes in the GnomAD database, including 7,279 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 0.30 (7279 hom., cov: 32)
• Consequence: MAGI2 NM_012301.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.04
• Publications: 2 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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.508 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.1045+10775T>C		intron	N/A	NP_036433.2
	MAGI2	NM_001301128.2		c.1045+10775T>C		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.1045+10775T>C		intron	N/A	ENSP00000346151.4
	MAGI2	ENST00000419488.5	TSL:1	c.1045+10775T>C		intron	N/A	ENSP00000405766.1
	MAGI2	ENST00000519748.5	TSL:1	c.-129+10775T>C		intron	N/A	ENSP00000486774.1

Frequencies

GnomAD3 genomes AF: 0.304 AC: 46045 AN: 151646 Hom.: 7279 Cov.: 32

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.310

Gnomad AMR AF: 0.352

Gnomad ASJ AF: 0.324

Gnomad EAS AF: 0.524

Gnomad SAS AF: 0.421

Gnomad FIN AF: 0.360

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.295

Gnomad OTH AF: 0.326

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

GnomAD4 genome AF: 0.304 AC: 46075 AN: 151764 Hom.: 7279 Cov.: 32 AF XY: 0.309 AC XY: 22903 AN XY: 74168

African (AFR) AF: 0.242 AC: 10035 AN: 41440

American (AMR) AF: 0.352 AC: 5357 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.324 AC: 1119 AN: 3454

East Asian (EAS) AF: 0.524 AC: 2677 AN: 5106

South Asian (SAS) AF: 0.421 AC: 2026 AN: 4816

European-Finnish (FIN) AF: 0.360 AC: 3804 AN: 10576

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.295 AC: 19992 AN: 67840

Other (OTH) AF: 0.323 AC: 682 AN: 2112

Alfa AF: 0.299 Hom.: 11678

Bravo AF: 0.300

Asia WGS AF: 0.445 AC: 1546 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.17
DANN	Benign	0.38
PhyloP100		-2.0
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs6951193; hg19: chr7-78108303;