3-65992417-C-T

Variant names:

• chr3-65992417-C-T
• rs6763833
• NM_001033057.2:c.313+45579G>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+45579G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.77 in 152,098 control chromosomes in the GnomAD database, including 45,525 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 0.77 (45525 hom., cov: 32)
• Consequence: MAGI1 NM_001033057.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.30
• Publications: 5 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]

LOC124900543 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.933 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAGI1	NM_001033057.2	c.313+45579G>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+45579G>A		intron_variant	Intron 1 of 22	1	NM_001033057.2	ENSP00000385450.2

Frequencies

GnomAD3 genomes AF: 0.770 AC: 116971 AN: 151980 Hom.: 45482 Cov.: 32

Gnomad AFR AF: 0.674

Gnomad AMI AF: 0.748

Gnomad AMR AF: 0.824

Gnomad ASJ AF: 0.856

Gnomad EAS AF: 0.955

Gnomad SAS AF: 0.641

Gnomad FIN AF: 0.866

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.791

Gnomad OTH AF: 0.778

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

GnomAD4 genome AF: 0.770 AC: 117062 AN: 152098 Hom.: 45525 Cov.: 32 AF XY: 0.771 AC XY: 57318 AN XY: 74350

African (AFR) AF: 0.674 AC: 27928 AN: 41436

American (AMR) AF: 0.825 AC: 12612 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.856 AC: 2971 AN: 3472

East Asian (EAS) AF: 0.955 AC: 4936 AN: 5166

South Asian (SAS) AF: 0.641 AC: 3090 AN: 4820

European-Finnish (FIN) AF: 0.866 AC: 9176 AN: 10592

Middle Eastern (MID) AF: 0.704 AC: 207 AN: 294

European-Non Finnish (NFE) AF: 0.791 AC: 53813 AN: 68004

Other (OTH) AF: 0.780 AC: 1648 AN: 2114

Alfa AF: 0.788 Hom.: 18086

Bravo AF: 0.767

Asia WGS AF: 0.765 AC: 2662 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.016
DANN	Benign	0.25
PhyloP100		-3.3
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.17		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: rs6763833; hg19: chr3-65978092;