rs11102637

chr1-113449170-G-A

Variant summary

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

The NM_001142782.2(MAGI3):c.316+57821G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.178 in 151,750 control chromosomes in the GnomAD database, including 3,148 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 0.18 (3148 hom., cov: 31)
• Consequence: MAGI3 NM_001142782.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0550

Genes affected

MAGI3 (HGNC:29647): (membrane associated guanylate kinase, WW and PDZ domain containing 3) Predicted to enable frizzled binding activity. Predicted to be involved in signal transduction. Predicted to act upstream of or within positive regulation of JUN kinase activity. Located in cell junction. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.611 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAGI3	NM_001142782.2	c.316+57821G>A		intron_variant		ENST00000307546.14

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAGI3	ENST00000307546.14	c.316+57821G>A		intron_variant		5	NM_001142782.2

Frequencies

GnomAD3 genomes AF: 0.178 AC: 27025 AN: 151640 Hom.: 3152 Cov.: 31

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.0691

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.630

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.241

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.197

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

GnomAD4 genome AF: 0.178 AC: 27019 AN: 151750 Hom.: 3148 Cov.: 31 AF XY: 0.184 AC XY: 13612 AN XY: 74172

Gnomad4 AFR AF: 0.122

Gnomad4 AMR AF: 0.235

Gnomad4 ASJ AF: 0.175

Gnomad4 EAS AF: 0.629

Gnomad4 SAS AF: 0.146

Gnomad4 FIN AF: 0.241

Gnomad4 NFE AF: 0.158

Gnomad4 OTH AF: 0.197

Alfa AF: 0.196 Hom.: 654

Bravo AF: 0.185

Asia WGS AF: 0.329 AC: 1141 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	2.1
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: rs11102637; hg19: chr1-113991792; COSMIC: COSV56831338; COSMIC: COSV56831338;