rs6537792

Variant names:

• chr1-113676979-G-C
• rs6537792
• NM_001142782.2:c.3189+3514G>C

Your query was ambiguous. Multiple possible variants found:

• chr1-113676979-G-C
• chr1-113676979-G-T

Variant summary

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

The NM_001142782.2(MAGI3):​c.3189+3514G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.753 in 152,060 control chromosomes in the GnomAD database, including 43,895 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 0.75 (43895 hom., cov: 31)
• Consequence: MAGI3 NM_001142782.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.872
• 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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.849 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAGI3	NM_001142782.2	c.3189+3514G>C		intron_variant	Intron 19 of 20	ENST00000307546.14	NP_001136254.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAGI3	ENST00000307546.14	c.3189+3514G>C		intron_variant	Intron 19 of 20	5	NM_001142782.2	ENSP00000304604.9
MAGI3	ENST00000369617.8	c.3264+3514G>C		intron_variant	Intron 20 of 21	1		ENSP00000358630.4
MAGI3	ENST00000369611.4	c.3189+3514G>C		intron_variant	Intron 19 of 20	1		ENSP00000358624.4
MAGI3	ENST00000369615.5	c.3189+3514G>C		intron_variant	Intron 19 of 21	5		ENSP00000358628.1

Frequencies

GnomAD3 genomes AF: 0.753 AC: 114405 AN: 151940 Hom.: 43845 Cov.: 31

Gnomad AFR AF: 0.857

Gnomad AMI AF: 0.795

Gnomad AMR AF: 0.633

Gnomad ASJ AF: 0.763

Gnomad EAS AF: 0.356

Gnomad SAS AF: 0.764

Gnomad FIN AF: 0.686

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.756

Gnomad OTH AF: 0.733

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

GnomAD4 genome AF: 0.753 AC: 114517 AN: 152060 Hom.: 43895 Cov.: 31 AF XY: 0.747 AC XY: 55497 AN XY: 74318

African (AFR) AF: 0.857 AC: 35560 AN: 41500

American (AMR) AF: 0.633 AC: 9671 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.763 AC: 2649 AN: 3472

East Asian (EAS) AF: 0.356 AC: 1838 AN: 5160

South Asian (SAS) AF: 0.764 AC: 3678 AN: 4814

European-Finnish (FIN) AF: 0.686 AC: 7248 AN: 10560

Middle Eastern (MID) AF: 0.724 AC: 213 AN: 294

European-Non Finnish (NFE) AF: 0.756 AC: 51392 AN: 67976

Other (OTH) AF: 0.733 AC: 1545 AN: 2108

Alfa AF: 0.751 Hom.: 5063

Bravo AF: 0.746

Asia WGS AF: 0.616 AC: 2143 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.11
DANN	Benign	0.34
PhyloP100		-0.87
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: rs6537792; hg19: chr1-114219601;