rs10858002

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001142782.2(MAGI3):​c.317-9205A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.293 in 152,140 control chromosomes in the GnomAD database, including 7,375 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 0.29 ( 7375 hom., cov: 33)

Consequence

MAGI3
NM_001142782.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0860
Variant links:
Genes affected
MAGI3 (HGNC:29647): (membrane associated guanylate kinase, WW and PDZ domain containing 3) Predicted to enable frizzled binding activity. Predicted to be involved in signal transduction. Predicted to act upstream of or within positive regulation of JUN kinase activity. Located in cell junction. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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 = 0.632 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
MAGI3NM_001142782.2 linkuse as main transcriptc.317-9205A>G intron_variant ENST00000307546.14 NP_001136254.1 Q5TCQ9-4

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
MAGI3ENST00000307546.14 linkuse as main transcriptc.317-9205A>G intron_variant 5 NM_001142782.2 ENSP00000304604.9 Q5TCQ9-4

Frequencies

GnomAD3 genomes
AF:
0.293
AC:
44580
AN:
152022
Hom.:
7378
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.161
Gnomad AMI
AF:
0.265
Gnomad AMR
AF:
0.406
Gnomad ASJ
AF:
0.279
Gnomad EAS
AF:
0.650
Gnomad SAS
AF:
0.265
Gnomad FIN
AF:
0.387
Gnomad MID
AF:
0.288
Gnomad NFE
AF:
0.310
Gnomad OTH
AF:
0.309
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.293
AC:
44587
AN:
152140
Hom.:
7375
Cov.:
33
AF XY:
0.300
AC XY:
22288
AN XY:
74376
show subpopulations
Gnomad4 AFR
AF:
0.161
Gnomad4 AMR
AF:
0.406
Gnomad4 ASJ
AF:
0.279
Gnomad4 EAS
AF:
0.650
Gnomad4 SAS
AF:
0.264
Gnomad4 FIN
AF:
0.387
Gnomad4 NFE
AF:
0.310
Gnomad4 OTH
AF:
0.309
Alfa
AF:
0.315
Hom.:
4580
Bravo
AF:
0.296
Asia WGS
AF:
0.418
AC:
1451
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
7.8
DANN
Benign
0.54

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs10858002; hg19: chr1-114082932; COSMIC: COSV56831638; API