NM_001033057.2:c.314-196820C>T

Variant names:

• chr3-65818908-G-A
• rs1108718
• NM_001033057.2:c.314-196820C>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.314-196820C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.477 in 151,976 control chromosomes in the GnomAD database, including 18,718 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 0.48 (18718 hom., cov: 32)
• Consequence: MAGI1 NM_001033057.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.521
• Publications: 4 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.734 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001033057.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAGI1	NM_001033057.2	MANE Select	c.314-196820C>T		intron	N/A	NP_001028229.1	Q96QZ7-2
	MAGI1	NM_001365903.2		c.314-196820C>T		intron	N/A	NP_001352832.1
	MAGI1	NM_001365904.2		c.314-196820C>T		intron	N/A	NP_001352833.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAGI1	ENST00000402939.7	TSL:1 MANE Select	c.314-196820C>T		intron	N/A	ENSP00000385450.2	Q96QZ7-2
	MAGI1	ENST00000330909.12	TSL:1	c.314-196820C>T		intron	N/A	ENSP00000331157.7	Q96QZ7-5
	MAGI1	ENST00000483466.5	TSL:1	c.314-196820C>T		intron	N/A	ENSP00000420323.1	Q96QZ7-3

Frequencies

GnomAD3 genomes AF: 0.478 AC: 72543 AN: 151858 Hom.: 18728 Cov.: 32

Gnomad AFR AF: 0.278

Gnomad AMI AF: 0.563

Gnomad AMR AF: 0.572

Gnomad ASJ AF: 0.485

Gnomad EAS AF: 0.753

Gnomad SAS AF: 0.533

Gnomad FIN AF: 0.574

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.537

Gnomad OTH AF: 0.478

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

GnomAD4 genome AF: 0.477 AC: 72553 AN: 151976 Hom.: 18718 Cov.: 32 AF XY: 0.482 AC XY: 35851 AN XY: 74308

African (AFR) AF: 0.278 AC: 11503 AN: 41432

American (AMR) AF: 0.572 AC: 8727 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.485 AC: 1685 AN: 3472

East Asian (EAS) AF: 0.754 AC: 3891 AN: 5162

South Asian (SAS) AF: 0.532 AC: 2563 AN: 4814

European-Finnish (FIN) AF: 0.574 AC: 6057 AN: 10560

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.537 AC: 36483 AN: 67954

Other (OTH) AF: 0.475 AC: 1003 AN: 2112

Alfa AF: 0.521 Hom.: 60742

Bravo AF: 0.472

Asia WGS AF: 0.622 AC: 2164 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.6
DANN	Benign	0.46
PhyloP100		-0.52
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: rs1108718; hg19: chr3-65804583;