Variant X-75784341-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_ModerateBP6_Very_StrongBP7BS2

The NM_138703.5(MAGEE2):c.711G>A(p.Glu237=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00627 in 1,210,095 control chromosomes in the GnomAD database, including 35 homozygotes. There are 2,435 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0046 ( 2 hom., 147 hem., cov: 23)

Exomes 𝑓: 0.0064 ( 33 hom. 2288 hem. )

Consequence

MAGEE2
NM_138703.5 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 2.46

Variant links:

Genes affected

MAGEE2 (HGNC:24935): (MAGE family member E2) This gene encodes a member of the E subfamily of MAGE (melanoma antigen-encoding gene) gene family. The gene is intronless and the encoded protein has two of the MAGE domains which are characteristic of MAGE family proteins. [provided by RefSeq, Sep 2011]

MAGEE2 links:

LOC107985664 (HGNC:):

LOC107985664 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.46).

BP6

Variant X-75784341-C-T is Benign according to our data. Variant chrX-75784341-C-T is described in ClinVar as [Benign]. Clinvar id is 771227.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=2.45 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 2 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAGEE2	NM_138703.5 linkuse as main transcript	c.711G>A	p.Glu237=	synonymous_variant	1/1	ENST00000373359.4	NP_619648.1
LOC107985664	XR_007068273.1 linkuse as main transcript	n.822-6951C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAGEE2	ENST00000373359.4 linkuse as main transcript	c.711G>A	p.Glu237=	synonymous_variant	1/1		NM_138703.5	ENSP00000362457	P1

Frequencies

GnomAD3 genomes

AF:

0.00462

AC:

516

AN:

111792

Hom.:

Cov.:

AF XY:

0.00433

AC XY:

147

AN XY:

33956

show subpopulations

Gnomad AFR

AF:

0.000620

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00773

Gnomad ASJ

AF:

0.00151

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00376

Gnomad MID

AF:

0.00422

Gnomad NFE

AF:

0.00711

Gnomad OTH

AF:

0.00597

GnomAD3 exomes

AF:

0.00432

AC:

792

AN:

183240

Hom.:

AF XY:

0.00452

AC XY:

306

AN XY:

67758

show subpopulations

Gnomad AFR exome

AF:

0.000608

Gnomad AMR exome

AF:

0.00219

Gnomad ASJ exome

AF:

0.00294

Gnomad EAS exome

AF:

0.0000722

Gnomad SAS exome

AF:

0.000839

Gnomad FIN exome

AF:

0.00287

Gnomad NFE exome

AF:

0.00751

Gnomad OTH exome

AF:

0.00552

GnomAD4 exome

AF:

0.00643

AC:

7067

AN:

1098248

Hom.:

Cov.:

AF XY:

0.00629

AC XY:

2288

AN XY:

363604

show subpopulations

Gnomad4 AFR exome

AF:

0.000909

Gnomad4 AMR exome

AF:

0.00219

Gnomad4 ASJ exome

AF:

0.00242

Gnomad4 EAS exome

AF:

0.0000331

Gnomad4 SAS exome

AF:

0.000739

Gnomad4 FIN exome

AF:

0.00336

Gnomad4 NFE exome

AF:

0.00769

Gnomad4 OTH exome

AF:

0.00503

GnomAD4 genome

AF:

0.00461

AC:

516

AN:

111847

Hom.:

Cov.:

AF XY:

0.00432

AC XY:

147

AN XY:

34021

show subpopulations

Gnomad4 AFR

AF:

0.000618

Gnomad4 AMR

AF:

0.00772

Gnomad4 ASJ

AF:

0.00151

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00376

Gnomad4 NFE

AF:

0.00711

Gnomad4 OTH

AF:

0.00589

Alfa

AF:

0.00564

Hom.:

Bravo

AF:

0.00428

EpiCase

AF:

0.00916

EpiControl

AF:

0.00913

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Mar 29, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.46

CADD

Benign

3.1

DANN

Benign

0.47

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.

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