chr3-65887431-G-A

Variant names:

• chr3-65887431-G-A
• rs9876471
• NM_001033057.2:c.313+150565C>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.313+150565C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.118 in 143,986 control chromosomes in the GnomAD database, including 1,112 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 0.12 (1112 hom., cov: 30)
• Consequence: MAGI1 NM_001033057.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.955
• 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]

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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.168 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAGI1	NM_001033057.2	MANE Select	c.313+150565C>T		intron	N/A	NP_001028229.1
	MAGI1	NM_001365903.2		c.313+150565C>T		intron	N/A	NP_001352832.1
	MAGI1	NM_001365904.2		c.313+150565C>T		intron	N/A	NP_001352833.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAGI1	ENST00000402939.7	TSL:1 MANE Select	c.313+150565C>T		intron	N/A	ENSP00000385450.2
	MAGI1	ENST00000330909.12	TSL:1	c.313+150565C>T		intron	N/A	ENSP00000331157.7
	MAGI1	ENST00000483466.5	TSL:1	c.313+150565C>T		intron	N/A	ENSP00000420323.1

Frequencies

GnomAD3 genomes AF: 0.118 AC: 16971 AN: 143976 Hom.: 1112 Cov.: 30

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.0515

Gnomad AMR AF: 0.0920

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.0996

Gnomad SAS AF: 0.135

Gnomad FIN AF: 0.0713

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.0995

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.118 AC: 16979 AN: 143986 Hom.: 1112 Cov.: 30 AF XY: 0.116 AC XY: 8104 AN XY: 69750

African (AFR) AF: 0.171 AC: 6702 AN: 39168

American (AMR) AF: 0.0919 AC: 1323 AN: 14392

Ashkenazi Jewish (ASJ) AF: 0.105 AC: 358 AN: 3414

East Asian (EAS) AF: 0.0997 AC: 497 AN: 4984

South Asian (SAS) AF: 0.136 AC: 622 AN: 4590

European-Finnish (FIN) AF: 0.0713 AC: 570 AN: 7994

Middle Eastern (MID) AF: 0.151 AC: 41 AN: 272

European-Non Finnish (NFE) AF: 0.0995 AC: 6596 AN: 66290

Other (OTH) AF: 0.113 AC: 224 AN: 1988

Alfa AF: 0.103 Hom.: 1455

Bravo AF: 0.118

Asia WGS AF: 0.135 AC: 468 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	16
DANN	Benign	0.76
PhyloP100		0.95
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: rs9876471; hg19: chr3-65873106;