chr22-27799614-A-ATGCTGC
Variant summary
Our verdict is Likely benign. The variant received -5 ACMG points: 0P and 5B. BP3BS2
The NM_002430.3(MN1):c.924_929dupGCAGCA(p.Gln308_Gln309dup) variant causes a disruptive inframe insertion change. The variant allele was found at a frequency of 0.00000719 in 1,390,046 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 0.0000072 ( 0 hom. )
Consequence
MN1
NM_002430.3 disruptive_inframe_insertion
NM_002430.3 disruptive_inframe_insertion
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 4.02
Publications
2 publications found
Genes affected
MN1 (HGNC:7180): (MN1 proto-oncogene, transcriptional regulator) Meningioma 1 (MN1) contains two sets of CAG repeats. It is disrupted by a balanced translocation (4;22) in a meningioma, and its inactivation may contribute to meningioma 32 pathogenesis. [provided by RefSeq, Jul 2008]
MN1 Gene-Disease associations (from GenCC):
- CEBALID syndromeInheritance: AD Classification: STRONG Submitted by: G2P, Ambry Genetics, Labcorp Genetics (formerly Invitae)
- familial meningiomaInheritance: AD Classification: LIMITED Submitted by: Ambry Genetics
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -5 ACMG points.
BP3
Nonframeshift variant in repetitive region in NM_002430.3
BS2
High AC in GnomAdExome4 at 10 AD gene.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| MN1 | NM_002430.3 | c.924_929dupGCAGCA | p.Gln308_Gln309dup | disruptive_inframe_insertion | Exon 1 of 2 | ENST00000302326.5 | NP_002421.3 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| MN1 | ENST00000302326.5 | c.924_929dupGCAGCA | p.Gln308_Gln309dup | disruptive_inframe_insertion | Exon 1 of 2 | 1 | NM_002430.3 | ENSP00000304956.4 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
33
GnomAD2 exomes AF: 0.00000891 AC: 1AN: 112286 AF XY: 0.0000168 show subpopulations
GnomAD2 exomes
AF:
AC:
1
AN:
112286
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.00000719 AC: 10AN: 1390046Hom.: 0 Cov.: 33 AF XY: 0.00000584 AC XY: 4AN XY: 685010 show subpopulations
GnomAD4 exome
AF:
AC:
10
AN:
1390046
Hom.:
Cov.:
33
AF XY:
AC XY:
4
AN XY:
685010
show subpopulations
African (AFR)
AF:
AC:
1
AN:
31410
American (AMR)
AF:
AC:
0
AN:
35088
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
24638
East Asian (EAS)
AF:
AC:
0
AN:
35600
South Asian (SAS)
AF:
AC:
0
AN:
77836
European-Finnish (FIN)
AF:
AC:
0
AN:
47958
Middle Eastern (MID)
AF:
AC:
0
AN:
5572
European-Non Finnish (NFE)
AF:
AC:
5
AN:
1074312
Other (OTH)
AF:
AC:
4
AN:
57632
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.485
Heterozygous variant carriers
0
1
2
3
4
5
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
45-50
50-55
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>80
Age
GnomAD4 genome
GnomAD4 genome
Cov.:
33
ClinVar
Not reported inComputational 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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