7-78586664-C-G

Position:

• chr7-78586664-C-G

Variant summary

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

The NM_012301.4(MAGI2):​c.538+40456G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.329 in 151,964 control chromosomes in the GnomAD database, including 8,244 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 0.33 (8244 hom., cov: 31)
• Consequence: MAGI2 NM_012301.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0580

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=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.348 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAGI2	NM_012301.4	c.538+40456G>C		intron_variant		ENST00000354212.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAGI2	ENST00000354212.9	c.538+40456G>C		intron_variant		1	NM_012301.4	P4

Frequencies

GnomAD3 genomes AF: 0.329 AC: 49917 AN: 151846 Hom.: 8246 Cov.: 31

Gnomad AFR AF: 0.292

Gnomad AMI AF: 0.356

Gnomad AMR AF: 0.325

Gnomad ASJ AF: 0.487

Gnomad EAS AF: 0.238

Gnomad SAS AF: 0.361

Gnomad FIN AF: 0.331

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.347

Gnomad OTH AF: 0.344

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

GnomAD4 genome AF: 0.329 AC: 49943 AN: 151964 Hom.: 8244 Cov.: 31 AF XY: 0.329 AC XY: 24431 AN XY: 74286

Gnomad4 AFR AF: 0.292

Gnomad4 AMR AF: 0.324

Gnomad4 ASJ AF: 0.487

Gnomad4 EAS AF: 0.238

Gnomad4 SAS AF: 0.362

Gnomad4 FIN AF: 0.331

Gnomad4 NFE AF: 0.347

Gnomad4 OTH AF: 0.343

Alfa AF: 0.211 Hom.: 461

Bravo AF: 0.324

Asia WGS AF: 0.287 AC: 997 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	1.3
DANN	Benign	0.78

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: rs759332; hg19: chr7-78215981;