3-65356704-G-A

Position:

• chr3-65356704-G-A

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2 BP6

The NM_001033057.2(MAGI1):​c.4063C>T​(p.Arg1355Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).

• Frequency: Genomes: not found (cov: 32)
• Consequence: MAGI1 NM_001033057.2 stop_gained
• Clinical Significance: Likely benign no assertion criteria provided B:1
• Conservation: PhyloP100: 1.62

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

Verdict is Uncertain_significance. Variant got 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP6: Variant 3-65356704-G-A is Benign according to our data. Variant chr3-65356704-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2681384.Status of the report is no_assertion_criteria_provided, 0 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAGI1	NM_001033057.2	c.4063C>T	p.Arg1355Ter	stop_gained	23/23	ENST00000402939.7	NP_001028229.1
MAGI1	NM_001365903.2	c.*372C>T		3_prime_UTR_variant	25/25		NP_001352832.1
MAGI1	NM_001365904.2	c.*372C>T		3_prime_UTR_variant	25/25		NP_001352833.1
MAGI1	NM_015520.2	c.*372C>T		3_prime_UTR_variant	25/25		NP_056335.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAGI1	ENST00000402939.7	c.4063C>T	p.Arg1355Ter	stop_gained	23/23	1	NM_001033057.2	ENSP00000385450	A2
MAGI1	ENST00000621418.4	c.3142C>T	p.Arg1048Ter	stop_gained	22/22	1		ENSP00000477591
MAGI1	ENST00000330909.12	c.*372C>T		3_prime_UTR_variant	25/25	1		ENSP00000331157	P4
MAGI1	ENST00000611645.4	c.*372C>T		3_prime_UTR_variant	24/24	1		ENSP00000480920

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

Submissions by phenotype

EBV-positive nodal T- and NK-cell lymphoma Benign:1

Likely benign, no assertion criteria provided

research

Department of Clinical Pathology, School of Medicine, Fujita Health University

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.45	D
BayesDel_noAF	Pathogenic	0.40
CADD	Pathogenic	37
DANN	Uncertain	1.0
Eigen	Uncertain	0.60
Eigen_PC	Uncertain	0.44
FATHMM_MKL	Uncertain	0.84	D
MutationTaster	Benign	1.0	D;D
Vest4		0.65
GERP RS		3.3
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.8

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr3-65342379; COSMIC: COSV100443540; COSMIC: COSV100443540;