7-78335471-C-T

Position:

• chr7-78335471-C-T

Variant summary

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

The NM_012301.4(MAGI2):​c.1408+8307G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.928 in 152,288 control chromosomes in the GnomAD database, including 65,795 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 0.93 (65795 hom., cov: 33)
• Consequence: MAGI2 NM_012301.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0860

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAGI2	NM_012301.4	c.1408+8307G>A		intron_variant		ENST00000354212.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAGI2	ENST00000354212.9	c.1408+8307G>A		intron_variant		1	NM_012301.4	P4

Frequencies

GnomAD3 genomes AF: 0.928 AC: 141263 AN: 152170 Hom.: 65731 Cov.: 33

Gnomad AFR AF: 0.983

Gnomad AMI AF: 0.924

Gnomad AMR AF: 0.937

Gnomad ASJ AF: 0.952

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.947

Gnomad FIN AF: 0.856

Gnomad MID AF: 0.943

Gnomad NFE AF: 0.897

Gnomad OTH AF: 0.923

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

GnomAD4 genome AF: 0.928 AC: 141387 AN: 152288 Hom.: 65795 Cov.: 33 AF XY: 0.928 AC XY: 69094 AN XY: 74456

Gnomad4 AFR AF: 0.983

Gnomad4 AMR AF: 0.937

Gnomad4 ASJ AF: 0.952

Gnomad4 EAS AF: 0.996

Gnomad4 SAS AF: 0.948

Gnomad4 FIN AF: 0.856

Gnomad4 NFE AF: 0.897

Gnomad4 OTH AF: 0.924

Alfa AF: 0.907 Hom.: 72435

Bravo AF: 0.937

Asia WGS AF: 0.967 AC: 3362 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.1
DANN	Benign	0.69

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: rs2691543; hg19: chr7-77964788;