rs10485909

chr7-78610431-G-Achr7-78610431-G-C

Variant summary

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

The NM_012301.4(MAGI2):c.538+16689C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0458 in 152,196 control chromosomes in the GnomAD database, including 227 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 0.046 (227 hom., cov: 32)
• Consequence: MAGI2 NM_012301.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0540

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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0727 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAGI2	NM_012301.4	c.538+16689C>T		intron_variant		ENST00000354212.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAGI2	ENST00000354212.9	c.538+16689C>T		intron_variant		1	NM_012301.4	P4

Frequencies

GnomAD3 genomes AF: 0.0458 AC: 6972 AN: 152078 Hom.: 225 Cov.: 32

Gnomad AFR AF: 0.0129

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.0585

Gnomad ASJ AF: 0.0389

Gnomad EAS AF: 0.0790

Gnomad SAS AF: 0.0104

Gnomad FIN AF: 0.0491

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0621

Gnomad OTH AF: 0.0464

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

GnomAD4 genome AF: 0.0458 AC: 6975 AN: 152196 Hom.: 227 Cov.: 32 AF XY: 0.0444 AC XY: 3305 AN XY: 74418

Gnomad4 AFR AF: 0.0129

Gnomad4 AMR AF: 0.0584

Gnomad4 ASJ AF: 0.0389

Gnomad4 EAS AF: 0.0790

Gnomad4 SAS AF: 0.0102

Gnomad4 FIN AF: 0.0491

Gnomad4 NFE AF: 0.0621

Gnomad4 OTH AF: 0.0478

Alfa AF: 0.0571 Hom.: 356

Bravo AF: 0.0461

Asia WGS AF: 0.0380 AC: 134 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.32
Dann	Benign	0.46

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: rs10485909; hg19: chr7-78239748;