3-65893414-G-T

Variant names:

• chr3-65893414-G-T
• rs264667
• NM_001033057.2:c.313+144582C>A

Variant summary

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

The NM_001033057.2(MAGI1):​c.313+144582C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.238 in 151,012 control chromosomes in the GnomAD database, including 6,302 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 0.24 (6302 hom., cov: 32)
• Consequence: MAGI1 NM_001033057.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.602
• Publications: 1 publications found

Genes affected

MAGI1 (HGNC:946): (membrane associated guanylate kinase, WW and PDZ domain containing 1) The protein encoded by this gene is a member of the membrane-associated guanylate kinase homologue (MAGUK) family. MAGUK proteins participate in the assembly of multiprotein complexes on the inner surface of the plasma membrane at regions of cell-cell contact. The product of this gene may play a role as scaffolding protein at cell-cell junctions. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]

MAGI1-IT1 (HGNC:42436): (MAGI1 intronic transcript 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.49 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAGI1	NM_001033057.2	c.313+144582C>A		intron_variant	Intron 1 of 22	ENST00000402939.7	NP_001028229.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAGI1	ENST00000402939.7	c.313+144582C>A		intron_variant	Intron 1 of 22	1	NM_001033057.2	ENSP00000385450.2

Frequencies

GnomAD3 genomes AF: 0.238 AC: 35916 AN: 150892 Hom.: 6270 Cov.: 32

Gnomad AFR AF: 0.496

Gnomad AMI AF: 0.110

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.112

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.0917

Gnomad MID AF: 0.217

Gnomad NFE AF: 0.143

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.238 AC: 35998 AN: 151012 Hom.: 6302 Cov.: 32 AF XY: 0.232 AC XY: 17093 AN XY: 73698

African (AFR) AF: 0.496 AC: 20433 AN: 41196

American (AMR) AF: 0.151 AC: 2288 AN: 15128

Ashkenazi Jewish (ASJ) AF: 0.199 AC: 688 AN: 3464

East Asian (EAS) AF: 0.112 AC: 575 AN: 5136

South Asian (SAS) AF: 0.162 AC: 776 AN: 4778

European-Finnish (FIN) AF: 0.0917 AC: 941 AN: 10264

Middle Eastern (MID) AF: 0.219 AC: 64 AN: 292

European-Non Finnish (NFE) AF: 0.143 AC: 9655 AN: 67740

Other (OTH) AF: 0.227 AC: 478 AN: 2102

Alfa AF: 0.0673 Hom.: 78

Bravo AF: 0.250

Asia WGS AF: 0.183 AC: 638 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.77
DANN	Benign	0.34
PhyloP100		-0.60
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: rs264667; hg19: chr3-65879089;