Variant chr22-27799614-ATGC-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP6BS2

The NM_002430.3(MN1):c.927_929del(p.Gln309del) variant causes a inframe deletion change. The variant allele was found at a frequency of 0.000467 in 1,519,040 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Benign,other (no stars).

Frequency

Genomes: 𝑓 0.000060 ( 0 hom., cov: 33)

Exomes 𝑓: 0.00051 ( 0 hom. )

Consequence

MN1
NM_002430.3 inframe_deletion

Scores

Not classified

Clinical Significance

Benign; other no assertion criteria provided B:1O:1

Conservation

PhyloP100: 6.72

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]

MN1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -5 ACMG points.

BP6

Variant 22-27799614-ATGC-A is Benign according to our data. Variant chr22-27799614-ATGC-A is described in ClinVar as [Benign, other]. Clinvar id is 438776.Status of the report is no_assertion_criteria_provided, 0 stars.

BS2

High AC in GnomAd4 at 9 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MN1	NM_002430.3 linkuse as main transcript	c.927_929del	p.Gln309del	inframe_deletion	1/2	ENST00000302326.5	NP_002421.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MN1	ENST00000302326.5 linkuse as main transcript	c.927_929del	p.Gln309del	inframe_deletion	1/2	1	NM_002430.3	ENSP00000304956	P1

Frequencies

GnomAD3 genomes

AF:

0.0000600

AC:

AN:

149982

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000491

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000104

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.000512

AC:

701

AN:

1369058

Hom.:

AF XY:

0.000604

AC XY:

407

AN XY:

673342

show subpopulations

Gnomad4 AFR exome

AF:

0.000551

Gnomad4 AMR exome

AF:

0.00176

Gnomad4 ASJ exome

AF:

0.00183

Gnomad4 EAS exome

AF:

0.0000862

Gnomad4 SAS exome

AF:

0.00185

Gnomad4 FIN exome

AF:

0.000832

Gnomad4 NFE exome

AF:

0.000349

Gnomad4 OTH exome

AF:

0.000512

GnomAD4 genome

AF:

0.0000600

AC:

AN:

149982

Hom.:

Cov.:

AF XY:

0.0000956

AC XY:

AN XY:

73210

show subpopulations

Gnomad4 AFR

AF:

0.0000491

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000104

Gnomad4 OTH

AF:

0.00

Bravo

AF:

0.0000604

ClinVar

Significance: Benign; other

Submissions summary: Benign:1Other:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

MN1-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

May 02, 2019

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Hepatoblastoma

Other:1

other, no assertion criteria provided

clinical testing

Donald Williams Parsons Laboratory, Baylor College of Medicine

May 01, 2016

- 3: Mutations in other consensus cancer genes, not currently considered targetable

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over