rs1159145

chr7-78835841-A-C

Variant summary

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

The NM_012301.4(MAGI2):c.418+171249T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0932 in 152,270 control chromosomes in the GnomAD database, including 775 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 0.093 (775 hom., cov: 32)
• Consequence: MAGI2 NM_012301.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.637

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.131 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAGI2	NM_012301.4	c.418+171249T>G		intron_variant		ENST00000354212.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAGI2	ENST00000354212.9	c.418+171249T>G		intron_variant		1	NM_012301.4	P4
MAGI2	ENST00000419488.5	c.418+171249T>G		intron_variant		1		A2
MAGI2	ENST00000522391.3	c.418+171249T>G		intron_variant		5		A2
MAGI2	ENST00000637441.1	c.418+171249T>G		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.0933 AC: 14202 AN: 152152 Hom.: 778 Cov.: 32

Gnomad AFR AF: 0.0384

Gnomad AMI AF: 0.0384

Gnomad AMR AF: 0.0790

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.0214

Gnomad SAS AF: 0.0418

Gnomad FIN AF: 0.129

Gnomad MID AF: 0.162

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.103

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

GnomAD4 genome AF: 0.0932 AC: 14196 AN: 152270 Hom.: 775 Cov.: 32 AF XY: 0.0912 AC XY: 6793 AN XY: 74452

Gnomad4 AFR AF: 0.0384

Gnomad4 AMR AF: 0.0788

Gnomad4 ASJ AF: 0.104

Gnomad4 EAS AF: 0.0212

Gnomad4 SAS AF: 0.0414

Gnomad4 FIN AF: 0.129

Gnomad4 NFE AF: 0.133

Gnomad4 OTH AF: 0.102

Alfa AF: 0.119 Hom.: 608

Bravo AF: 0.0890

Asia WGS AF: 0.0400 AC: 140 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	7.5
Dann	Benign	0.57

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: rs1159145; hg19: chr7-78465157;