Variant X-30242489-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2

The NM_002367.4(MAGEB4):c.354G>A(p.Gln118=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00837 in 1,209,082 control chromosomes in the GnomAD database, including 48 homozygotes. There are 3,338 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0061 ( 5 hom., 208 hem., cov: 23)

Exomes 𝑓: 0.0086 ( 43 hom. 3130 hem. )

Consequence

MAGEB4
NM_002367.4 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -1.18

Variant links:

Genes affected

MAGEB4 (HGNC:6811): (MAGE family member B4) This gene is a member of the MAGEB gene family. The members of this family have their entire coding sequences located in the last exon, and the encoded proteins show 50 to 68% sequence identity to each other. The promoters and first exons of the MAGEB genes show considerable variability, suggesting that the existence of this gene family enables the same function to be expressed under different transcriptional controls. The MAGEB genes are clustered on chromosome Xp22-p21. This gene sequence ends in the first intron of MAGEB1, another family member. This gene is expressed in testis. [provided by RefSeq, Jul 2008]

MAGEB4 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -17 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BP6

Variant X-30242489-G-A is Benign according to our data. Variant chrX-30242489-G-A is described in ClinVar as [Benign]. Clinvar id is 771224.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-1.18 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 5 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAGEB4	NM_002367.4 linkuse as main transcript	c.354G>A	p.Gln118=	synonymous_variant	1/1	ENST00000378982.4	NP_002358.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAGEB4	ENST00000378982.4 linkuse as main transcript	c.354G>A	p.Gln118=	synonymous_variant	1/1		NM_002367.4	ENSP00000368266	P1

Frequencies

GnomAD3 genomes

AF:

0.00606

AC:

681

AN:

112384

Hom.:

Cov.:

AF XY:

0.00602

AC XY:

208

AN XY:

34532

show subpopulations

Gnomad AFR

AF:

0.00110

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00253

Gnomad ASJ

AF:

0.0471

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00828

Gnomad FIN

AF:

0.00146

Gnomad MID

AF:

0.0167

Gnomad NFE

AF:

0.00839

Gnomad OTH

AF:

0.00854

GnomAD3 exomes

AF:

0.00751

AC:

1350

AN:

179694

Hom.:

AF XY:

0.00764

AC XY:

492

AN XY:

64356

show subpopulations

Gnomad AFR exome

AF:

0.00101

Gnomad AMR exome

AF:

0.00147

Gnomad ASJ exome

AF:

0.0491

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00768

Gnomad FIN exome

AF:

0.00202

Gnomad NFE exome

AF:

0.00891

Gnomad OTH exome

AF:

0.0107

GnomAD4 exome

AF:

0.00861

AC:

9440

AN:

1096644

Hom.:

Cov.:

AF XY:

0.00864

AC XY:

3130

AN XY:

362064

show subpopulations

Gnomad4 AFR exome

AF:

0.000949

Gnomad4 AMR exome

AF:

0.00139

Gnomad4 ASJ exome

AF:

0.0487

Gnomad4 EAS exome

AF:

0.0000332

Gnomad4 SAS exome

AF:

0.00880

Gnomad4 FIN exome

AF:

0.00267

Gnomad4 NFE exome

AF:

0.00862

Gnomad4 OTH exome

AF:

0.0113

GnomAD4 genome

AF:

0.00606

AC:

681

AN:

112438

Hom.:

Cov.:

AF XY:

0.00601

AC XY:

208

AN XY:

34596

show subpopulations

Gnomad4 AFR

AF:

0.00110

Gnomad4 AMR

AF:

0.00253

Gnomad4 ASJ

AF:

0.0471

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00831

Gnomad4 FIN

AF:

0.00146

Gnomad4 NFE

AF:

0.00839

Gnomad4 OTH

AF:

0.00844

Alfa

AF:

0.0117

Hom.:

Bravo

AF:

0.00601

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	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Dec 31, 2019	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

1.2

DANN

Benign

0.82

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