rs10260177

chr7-78446317-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.1045+43444A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.871 in 151,966 control chromosomes in the GnomAD database, including 57,726 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 0.87 (57726 hom., cov: 31)
• Consequence: MAGI2 NM_012301.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.918 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAGI2	NM_012301.4	c.1045+43444A>G		intron_variant		ENST00000354212.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAGI2	ENST00000354212.9	c.1045+43444A>G		intron_variant		1	NM_012301.4	P4
	ENST00000648775.1	n.58+2625A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.871 AC: 132231 AN: 151848 Hom.: 57700 Cov.: 31

Gnomad AFR AF: 0.806

Gnomad AMI AF: 0.924

Gnomad AMR AF: 0.927

Gnomad ASJ AF: 0.920

Gnomad EAS AF: 0.940

Gnomad SAS AF: 0.864

Gnomad FIN AF: 0.879

Gnomad MID AF: 0.937

Gnomad NFE AF: 0.887

Gnomad OTH AF: 0.887

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

GnomAD4 genome AF: 0.871 AC: 132310 AN: 151966 Hom.: 57726 Cov.: 31 AF XY: 0.873 AC XY: 64825 AN XY: 74284

Gnomad4 AFR AF: 0.806

Gnomad4 AMR AF: 0.927

Gnomad4 ASJ AF: 0.920

Gnomad4 EAS AF: 0.940

Gnomad4 SAS AF: 0.864

Gnomad4 FIN AF: 0.879

Gnomad4 NFE AF: 0.887

Gnomad4 OTH AF: 0.883

Alfa AF: 0.880 Hom.: 16296

Bravo AF: 0.874

Asia WGS AF: 0.855 AC: 2970 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	2.2
Dann	Benign	0.43

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: rs10260177; hg19: chr7-78075634;