22-27750781-G-GA

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The ENST00000302326.5(MN1):​c.*133_*134insT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.118 in 463,614 control chromosomes in the GnomAD database, including 80 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.076 ( 52 hom., cov: 23)
Exomes 𝑓: 0.12 ( 28 hom. )

Consequence

MN1
ENST00000302326.5 3_prime_UTR

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.0310
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6
Variant 22-27750781-G-GA is Benign according to our data. Variant chr22-27750781-G-GA is described in ClinVar as [Benign]. Clinvar id is 1261235.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.188 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
MN1NM_002430.3 linkuse as main transcriptc.*133_*134insT 3_prime_UTR_variant 2/2 ENST00000302326.5 NP_002421.3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
MN1ENST00000302326.5 linkuse as main transcriptc.*133_*134insT 3_prime_UTR_variant 2/21 NM_002430.3 ENSP00000304956 P1
MN1ENST00000497225.1 linkuse as main transcriptn.452_453insT non_coding_transcript_exon_variant 2/21
MN1ENST00000703102.1 linkuse as main transcriptn.621_622insT non_coding_transcript_exon_variant 2/2
MN1ENST00000424656.1 linkuse as main transcriptc.*133_*134insT 3_prime_UTR_variant, NMD_transcript_variant 2/35 ENSP00000397805

Frequencies

GnomAD3 genomes
AF:
0.0758
AC:
3129
AN:
41258
Hom.:
52
Cov.:
23
show subpopulations
Gnomad AFR
AF:
0.0152
Gnomad AMI
AF:
0.0184
Gnomad AMR
AF:
0.0413
Gnomad ASJ
AF:
0.206
Gnomad EAS
AF:
0.204
Gnomad SAS
AF:
0.0273
Gnomad FIN
AF:
0.146
Gnomad MID
AF:
0.105
Gnomad NFE
AF:
0.0878
Gnomad OTH
AF:
0.0625
GnomAD4 exome
AF:
0.122
AC:
51642
AN:
422328
Hom.:
28
Cov.:
6
AF XY:
0.124
AC XY:
26424
AN XY:
213002
show subpopulations
Gnomad4 AFR exome
AF:
0.0443
Gnomad4 AMR exome
AF:
0.107
Gnomad4 ASJ exome
AF:
0.153
Gnomad4 EAS exome
AF:
0.233
Gnomad4 SAS exome
AF:
0.122
Gnomad4 FIN exome
AF:
0.144
Gnomad4 NFE exome
AF:
0.116
Gnomad4 OTH exome
AF:
0.125
GnomAD4 genome
AF:
0.0758
AC:
3129
AN:
41286
Hom.:
52
Cov.:
23
AF XY:
0.0789
AC XY:
1538
AN XY:
19502
show subpopulations
Gnomad4 AFR
AF:
0.0151
Gnomad4 AMR
AF:
0.0413
Gnomad4 ASJ
AF:
0.206
Gnomad4 EAS
AF:
0.204
Gnomad4 SAS
AF:
0.0267
Gnomad4 FIN
AF:
0.146
Gnomad4 NFE
AF:
0.0878
Gnomad4 OTH
AF:
0.0620

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxMay 16, 2021- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

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: rs377485634; hg19: chr22-28146769; API