Variant 3-184711345-ATCCTCCTCCTCC-ATCCTCCTCCTCCTCCTCC details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2

The NM_022149.5(MAGEF1):c.471_476dupGGAGGA(p.Glu157_Glu158dup) variant causes a disruptive inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00226 in 1,567,536 control chromosomes in the GnomAD database, including 36 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0085 ( 12 hom., cov: 0)

Exomes 𝑓: 0.0016 ( 24 hom. )

Consequence

MAGEF1
NM_022149.5 disruptive_inframe_insertion

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.156

Variant links:

Genes affected

MAGEF1 (HGNC:29639): (MAGE family member F1) This intronless gene encodes a member of the MAGE superfamily. It is ubiquitously expressed in normal tissues and in tumor cells. This gene includes a microsatellite repeat in the coding region. [provided by RefSeq, Jul 2008]

MAGEF1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 3-184711345-A-ATCCTCC is Benign according to our data. Variant chr3-184711345-A-ATCCTCC is described in ClinVar as [Benign]. Clinvar id is 403067.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00855 (1287/150552) while in subpopulation AFR AF= 0.0277 (1135/40980). AF 95% confidence interval is 0.0264. There are 12 homozygotes in gnomad4. There are 609 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 12 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAGEF1	NM_022149.5 linkuse as main transcript	c.471_476dupGGAGGA	p.Glu157_Glu158dup	disruptive_inframe_insertion	1/1	ENST00000317897.5	NP_071432.2	Q9HAY2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAGEF1	ENST00000317897.5 linkuse as main transcript	c.471_476dupGGAGGA	p.Glu157_Glu158dup	disruptive_inframe_insertion	1/1	6	NM_022149.5	ENSP00000315064.3		Q9HAY2

Frequencies

GnomAD3 genomes

AF:

0.00853

AC:

1283

AN:

150432

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0277

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00284

Gnomad ASJ

AF:

0.00984

Gnomad EAS

AF:

0.000392

Gnomad SAS

AF:

0.000632

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00325

Gnomad NFE

AF:

0.000800

Gnomad OTH

AF:

0.00674

GnomAD3 exomes

AF:

0.00301

AC:

730

AN:

242436

Hom.:

AF XY:

0.00243

AC XY:

319

AN XY:

131400

show subpopulations

Gnomad AFR exome

AF:

0.0304

Gnomad AMR exome

AF:

0.00152

Gnomad ASJ exome

AF:

0.0117

Gnomad EAS exome

AF:

0.000441

Gnomad SAS exome

AF:

0.000235

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000603

Gnomad OTH exome

AF:

0.00204

GnomAD4 exome

AF:

0.00159

AC:

2257

AN:

1416984

Hom.:

Cov.:

AF XY:

0.00147

AC XY:

1035

AN XY:

705666

show subpopulations

Gnomad4 AFR exome

AF:

0.0332

Gnomad4 AMR exome

AF:

0.00180

Gnomad4 ASJ exome

AF:

0.0121

Gnomad4 EAS exome

AF:

0.000253

Gnomad4 SAS exome

AF:

0.000248

Gnomad4 FIN exome

AF:

0.0000196

Gnomad4 NFE exome

AF:

0.000510

Gnomad4 OTH exome

AF:

0.00297

GnomAD4 genome

AF:

0.00855

AC:

1287

AN:

150552

Hom.:

Cov.:

AF XY:

0.00828

AC XY:

609

AN XY:

73526

show subpopulations

Gnomad4 AFR

AF:

0.0277

Gnomad4 AMR

AF:

0.00284

Gnomad4 ASJ

AF:

0.00984

Gnomad4 EAS

AF:

0.000392

Gnomad4 SAS

AF:

0.000633

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000800

Gnomad4 OTH

AF:

0.00715

EpiCase

AF:

0.000709

EpiControl

AF:

0.000949

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 29, 2016

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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