chr7-78506875-T-C

Position:

• chr7-78506875-T-C

Variant summary

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

The NM_012301.4(MAGI2):​c.755-5088A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.689 in 152,170 control chromosomes in the GnomAD database, including 36,911 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 0.69 (36911 hom., cov: 32)
• Consequence: MAGI2 NM_012301.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.64

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.836 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAGI2	NM_012301.4	c.755-5088A>G		intron_variant		ENST00000354212.9	NP_036433.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAGI2	ENST00000354212.9	c.755-5088A>G		intron_variant		1	NM_012301.4	ENSP00000346151.4

Frequencies

GnomAD3 genomes AF: 0.689 AC: 104690 AN: 152052 Hom.: 36857 Cov.: 32

Gnomad AFR AF: 0.843

Gnomad AMI AF: 0.595

Gnomad AMR AF: 0.597

Gnomad ASJ AF: 0.687

Gnomad EAS AF: 0.468

Gnomad SAS AF: 0.732

Gnomad FIN AF: 0.617

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.642

Gnomad OTH AF: 0.674

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

GnomAD4 genome AF: 0.689 AC: 104802 AN: 152170 Hom.: 36911 Cov.: 32 AF XY: 0.686 AC XY: 50988 AN XY: 74380

Gnomad4 AFR AF: 0.843

Gnomad4 AMR AF: 0.597

Gnomad4 ASJ AF: 0.687

Gnomad4 EAS AF: 0.467

Gnomad4 SAS AF: 0.732

Gnomad4 FIN AF: 0.617

Gnomad4 NFE AF: 0.642

Gnomad4 OTH AF: 0.673

Alfa AF: 0.644 Hom.: 53614

Bravo AF: 0.686

Asia WGS AF: 0.645 AC: 2244 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.029
DANN	Benign	0.49

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: rs2110630; hg19: chr7-78136192;