7-78019494-TGCC-TGCCGCCGCC
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM4BP6_Moderate
The NM_012301.4(MAGI2):c.4183_4188dupGGCGGC(p.Gly1395_Gly1396dup) variant causes a conservative inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000613 in 979,496 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000035 ( 0 hom., cov: 30)
Exomes 𝑓: 0.0000012 ( 0 hom. )
Consequence
MAGI2
NM_012301.4 conservative_inframe_insertion
NM_012301.4 conservative_inframe_insertion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.249
Publications
0 publications found
Genes affected
MAGI2 (HGNC:18957): (membrane associated guanylate kinase, WW and PDZ domain containing 2) The protein encoded by this gene interacts with atrophin-1. Atrophin-1 contains a polyglutamine repeat, expansion of which is responsible for dentatorubral and pallidoluysian atrophy. This encoded protein is characterized by two WW domains, a guanylate kinase-like domain, and multiple PDZ domains. It has structural similarity to the membrane-associated guanylate kinase homologue (MAGUK) family. [provided by RefSeq, Jul 2008]
MAGI2 Gene-Disease associations (from GenCC):
- nephrotic syndrome 15Inheritance: AR Classification: STRONG, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics
- familial idiopathic steroid-resistant nephrotic syndromeInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- genetic developmental and epileptic encephalopathyInheritance: AD Classification: LIMITED Submitted by: G2P
- epilepsyInheritance: AD Classification: NO_KNOWN Submitted by: ClinGen
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 0 ACMG points.
PM4
Nonframeshift variant in NON repetitive region in NM_012301.4.
BP6
Variant 7-78019494-T-TGCCGCC is Benign according to our data. Variant chr7-78019494-T-TGCCGCC is described in ClinVar as Likely_benign. ClinVar VariationId is 211418.Status of the report is criteria_provided_single_submitter, 1 stars.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_012301.4. 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 |
|---|---|---|---|---|---|---|---|---|---|
| MAGI2 | MANE Select | c.4183_4188dupGGCGGC | p.Gly1395_Gly1396dup | conservative_inframe_insertion | Exon 22 of 22 | NP_036433.2 | |||
| MAGI2 | c.4141_4146dupGGCGGC | p.Gly1381_Gly1382dup | conservative_inframe_insertion | Exon 21 of 21 | NP_001288057.1 | Q86UL8-2 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| MAGI2 | TSL:1 MANE Select | c.4183_4188dupGGCGGC | p.Gly1395_Gly1396dup | conservative_inframe_insertion | Exon 22 of 22 | ENSP00000346151.4 | Q86UL8-1 | ||
| MAGI2 | TSL:1 | c.4141_4146dupGGCGGC | p.Gly1381_Gly1382dup | conservative_inframe_insertion | Exon 21 of 21 | ENSP00000405766.1 | Q86UL8-2 | ||
| MAGI2 | TSL:5 | c.*420_*425dupGGCGGC | 3_prime_UTR | Exon 23 of 23 | ENSP00000428389.1 | E7EWI0 |
Frequencies
GnomAD3 genomes 0.0000345 AC: 5AN: 144846Hom.: 0 Cov.: 30 show subpopulations
GnomAD3 genomes
AF:
AC:
5
AN:
144846
Hom.:
Cov.:
30
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.00000120 AC: 1AN: 834650Hom.: 0 Cov.: 30 AF XY: 0.00000259 AC XY: 1AN XY: 385730 show subpopulations
GnomAD4 exome
AF:
AC:
1
AN:
834650
Hom.:
Cov.:
30
AF XY:
AC XY:
1
AN XY:
385730
show subpopulations
African (AFR)
AF:
AC:
0
AN:
15792
American (AMR)
AF:
AC:
0
AN:
1002
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
5164
East Asian (EAS)
AF:
AC:
0
AN:
3688
South Asian (SAS)
AF:
AC:
0
AN:
17132
European-Finnish (FIN)
AF:
AC:
0
AN:
288
Middle Eastern (MID)
AF:
AC:
0
AN:
1620
European-Non Finnish (NFE)
AF:
AC:
1
AN:
762634
Other (OTH)
AF:
AC:
0
AN:
27330
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.425
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
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>80
Age
GnomAD4 genome 0.0000345 AC: 5AN: 144846Hom.: 0 Cov.: 30 AF XY: 0.0000142 AC XY: 1AN XY: 70400 show subpopulations
GnomAD4 genome
AF:
AC:
5
AN:
144846
Hom.:
Cov.:
30
AF XY:
AC XY:
1
AN XY:
70400
show subpopulations
African (AFR)
AF:
AC:
2
AN:
40506
American (AMR)
AF:
AC:
2
AN:
14662
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3382
East Asian (EAS)
AF:
AC:
0
AN:
4930
South Asian (SAS)
AF:
AC:
0
AN:
4706
European-Finnish (FIN)
AF:
AC:
0
AN:
8124
Middle Eastern (MID)
AF:
AC:
0
AN:
308
European-Non Finnish (NFE)
AF:
AC:
1
AN:
65326
Other (OTH)
AF:
AC:
0
AN:
1998
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.495
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
ClinVar
ClinVar submissions
View on ClinVar Significance:Likely benign
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
-
1
not specified (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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