rs884067

Variant names:

• chr3-65667087-G-A
• rs884067
• NM_001033057.2:c.314-44999C>T

Your query was ambiguous. Multiple possible variants found:

• chr3-65667087-G-A
• chr3-65667087-G-T

Variant summary

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

The NM_001033057.2(MAGI1):​c.314-44999C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.315 in 152,054 control chromosomes in the GnomAD database, including 7,737 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 0.32 (7737 hom., cov: 33)
• Consequence: MAGI1 NM_001033057.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.12
• Publications: 3 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]

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 (NFE) allele frequency at 95% confidence interval = 0.348 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAGI1	NM_001033057.2	c.314-44999C>T		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.314-44999C>T		intron_variant	Intron 1 of 22	1	NM_001033057.2	ENSP00000385450.2

Frequencies

GnomAD3 genomes AF: 0.315 AC: 47889 AN: 151936 Hom.: 7724 Cov.: 33

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.313

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.348

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.331

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.303

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

GnomAD4 genome AF: 0.315 AC: 47929 AN: 152054 Hom.: 7737 Cov.: 33 AF XY: 0.310 AC XY: 23066 AN XY: 74322

African (AFR) AF: 0.276 AC: 11455 AN: 41486

American (AMR) AF: 0.274 AC: 4180 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.218 AC: 756 AN: 3464

East Asian (EAS) AF: 0.347 AC: 1794 AN: 5164

South Asian (SAS) AF: 0.275 AC: 1324 AN: 4814

European-Finnish (FIN) AF: 0.331 AC: 3502 AN: 10566

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.352 AC: 23926 AN: 67974

Other (OTH) AF: 0.306 AC: 644 AN: 2104

Alfa AF: 0.334 Hom.: 14829

Bravo AF: 0.311

Asia WGS AF: 0.349 AC: 1214 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	0.26
DANN	Benign	0.71
PhyloP100		-2.1
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: rs884067; hg19: chr3-65652762;