1-113630788-A-G

Variant names:

• chr1-113630788-A-G
• rs1230666
• NM_001142782.2:c.1360+7794A>G

Variant summary

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

The NM_001142782.2(MAGI3):​c.1360+7794A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.905 in 152,016 control chromosomes in the GnomAD database, including 62,495 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 0.90 (62495 hom., cov: 29)
• Consequence: MAGI3 NM_001142782.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.574
• Publications: 39 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001142782.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAGI3	NM_001142782.2	MANE Select	c.1360+7794A>G		intron	N/A	NP_001136254.1
	MAGI3	NM_152900.3		c.1360+7794A>G		intron	N/A	NP_690864.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAGI3	ENST00000307546.14	TSL:5 MANE Select	c.1360+7794A>G		intron	N/A	ENSP00000304604.9
	MAGI3	ENST00000369617.8	TSL:1	c.1435+7794A>G		intron	N/A	ENSP00000358630.4
	MAGI3	ENST00000369611.4	TSL:1	c.1360+7794A>G		intron	N/A	ENSP00000358624.4

Frequencies

GnomAD3 genomes AF: 0.905 AC: 137431 AN: 151898 Hom.: 62434 Cov.: 29

Gnomad AFR AF: 0.976

Gnomad AMI AF: 0.916

Gnomad AMR AF: 0.924

Gnomad ASJ AF: 0.922

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.980

Gnomad FIN AF: 0.835

Gnomad MID AF: 0.870

Gnomad NFE AF: 0.855

Gnomad OTH AF: 0.904

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

GnomAD4 genome AF: 0.905 AC: 137551 AN: 152016 Hom.: 62495 Cov.: 29 AF XY: 0.907 AC XY: 67355 AN XY: 74282

African (AFR) AF: 0.976 AC: 40511 AN: 41504

American (AMR) AF: 0.924 AC: 14126 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.922 AC: 3196 AN: 3468

East Asian (EAS) AF: 1.00 AC: 5134 AN: 5136

South Asian (SAS) AF: 0.980 AC: 4701 AN: 4798

European-Finnish (FIN) AF: 0.835 AC: 8809 AN: 10548

Middle Eastern (MID) AF: 0.874 AC: 257 AN: 294

European-Non Finnish (NFE) AF: 0.855 AC: 58069 AN: 67950

Other (OTH) AF: 0.906 AC: 1913 AN: 2112

Alfa AF: 0.883 Hom.: 89133

Bravo AF: 0.915

Asia WGS AF: 0.984 AC: 3421 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.0
DANN	Benign	0.21
PhyloP100		-0.57
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: rs1230666; hg19: chr1-114173410;