NM_001142782.2:c.316+7194G>A

Variant names:

• chr1-113398543-G-A
• rs1112085
• NM_001142782.2:c.316+7194G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001142782.2(MAGI3):​c.316+7194G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.179 in 151,928 control chromosomes in the GnomAD database, including 3,162 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 (3162 hom., cov: 32)
• Consequence: MAGI3 NM_001142782.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.517
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.609 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAGI3	NM_001142782.2	c.316+7194G>A		intron_variant	Intron 1 of 20	ENST00000307546.14	NP_001136254.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAGI3	ENST00000307546.14	c.316+7194G>A		intron_variant	Intron 1 of 20	5	NM_001142782.2	ENSP00000304604.9

Frequencies

GnomAD3 genomes AF: 0.179 AC: 27181 AN: 151810 Hom.: 3166 Cov.: 32

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.0692

Gnomad AMR AF: 0.236

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.628

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.244

Gnomad MID AF: 0.188

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.198

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

GnomAD4 genome AF: 0.179 AC: 27176 AN: 151928 Hom.: 3162 Cov.: 32 AF XY: 0.184 AC XY: 13686 AN XY: 74230

African (AFR) AF: 0.124 AC: 5142 AN: 41450

American (AMR) AF: 0.236 AC: 3592 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.175 AC: 608 AN: 3470

East Asian (EAS) AF: 0.627 AC: 3233 AN: 5160

South Asian (SAS) AF: 0.147 AC: 710 AN: 4826

European-Finnish (FIN) AF: 0.244 AC: 2564 AN: 10524

Middle Eastern (MID) AF: 0.185 AC: 54 AN: 292

European-Non Finnish (NFE) AF: 0.159 AC: 10793 AN: 67942

Other (OTH) AF: 0.198 AC: 417 AN: 2106

Alfa AF: 0.169 Hom.: 324

Bravo AF: 0.186

Asia WGS AF: 0.328 AC: 1137 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	0.33
DANN	Benign	0.76
PhyloP100		-0.52
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1112085; hg19: chr1-113941165; COSMIC: COSV56831152;