rs9876471

chr3-65887431-G-A

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAGI1	NM_001033057.2	c.313+150565C>T		intron_variant		ENST00000402939.7
MAGI1-IT1	NR_145422.1	n.332-12381C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAGI1	ENST00000402939.7	c.313+150565C>T		intron_variant		1	NM_001033057.2	A2
MAGI1-IT1	ENST00000460754.1	n.332-12381C>T		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.171

Gnomad4 AMR AF: 0.0919

Gnomad4 ASJ AF: 0.105

Gnomad4 EAS AF: 0.0997

Gnomad4 SAS AF: 0.136

Gnomad4 FIN AF: 0.0713

Gnomad4 NFE AF: 0.0995

Gnomad4 OTH AF: 0.113

Alfa AF: 0.102 Hom.: 1139

Bravo AF: 0.118

Asia WGS AF: 0.135 AC: 468 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	16
Dann	Benign	0.76

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

Publications

LitVar

Other links and lift over

dbSNP: rs9876471; hg19: chr3-65873106;