Variant X-152767308-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate

The ENST00000329342.10(MAGEA6):c.343A>G(p.Lys115Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 5/7 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0030 ( 2 hom., 49 hem., cov: 20)

Exomes 𝑓: 0.0020 ( 8 hom. 844 hem. )

Failed GnomAD Quality Control

Consequence

MAGEA6
ENST00000329342.10 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.770

Variant links:

Genes affected

MAGEA6 (HGNC:6804): (MAGE family member A6) This gene is a member of the MAGEA gene family. The members of this family encode proteins with 50 to 80% sequence identity to each other. The promoters and first exons of the MAGEA genes show considerable variability, suggesting that the existence of this gene family enables the same function to be expressed under different transcriptional controls. The MAGEA genes are clustered at chromosomal location Xq28. They have been implicated in some hereditary disorders, such as dyskeratosis congenita. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2013]

MAGEA6 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.051576465).

BP6

Variant X-152767308-T-C is Benign according to our data. Variant chrX-152767308-T-C is described in ClinVar as [Benign]. Clinvar id is 777745.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAGEA6	NM_005363.5 linkuse as main transcript	c.343A>G	p.Lys115Glu	missense_variant	3/3	ENST00000329342.10	NP_005354.1
MAGEA6	NM_175868.4 linkuse as main transcript	c.343A>G	p.Lys115Glu	missense_variant	3/3		NP_787064.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris
MAGEA6	ENST00000329342.10 linkuse as main transcript	c.343A>G	p.Lys115Glu	missense_variant	3/3	1	NM_005363.5	ENSP00000329199	P1
MAGEA6	ENST00000616035.4 linkuse as main transcript	c.343A>G	p.Lys115Glu	missense_variant	3/3	5		ENSP00000480637	P1
MAGEA6	ENST00000457643.1 linkuse as main transcript	c.343A>G	p.Lys115Glu	missense_variant	4/4	3		ENSP00000401806
MAGEA6	ENST00000412733.1 linkuse as main transcript	c.343A>G	p.Lys115Glu	missense_variant	3/3	5		ENSP00000403303

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

332

AN:

110788

Hom.:

Cov.:

AF XY:

0.00145

AC XY:

AN XY:

33096

FAILED QC

Gnomad AFR

AF:

0.00458

Gnomad AMI

AF:

0.0437

Gnomad AMR

AF:

0.00285

Gnomad ASJ

AF:

0.00114

Gnomad EAS

AF:

0.00709

Gnomad SAS

AF:

0.00236

Gnomad FIN

AF:

0.000166

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00182

Gnomad OTH

AF:

0.00203

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00195

AC:

2143

AN:

1096172

Hom.:

Cov.:

AF XY:

0.00233

AC XY:

844

AN XY:

362456

show subpopulations

Gnomad4 AFR exome

AF:

0.00512

Gnomad4 AMR exome

AF:

0.00327

Gnomad4 ASJ exome

AF:

0.00135

Gnomad4 EAS exome

AF:

0.00940

Gnomad4 SAS exome

AF:

0.00391

Gnomad4 FIN exome

AF:

0.000370

Gnomad4 NFE exome

AF:

0.00147

Gnomad4 OTH exome

AF:

0.00237

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00299

AC:

331

AN:

110840

Hom.:

Cov.:

AF XY:

0.00148

AC XY:

AN XY:

33158

show subpopulations

Gnomad4 AFR

AF:

0.00457

Gnomad4 AMR

AF:

0.00275

Gnomad4 ASJ

AF:

0.00114

Gnomad4 EAS

AF:

0.00683

Gnomad4 SAS

AF:

0.00276

Gnomad4 FIN

AF:

0.000166

Gnomad4 NFE

AF:

0.00182

Gnomad4 OTH

AF:

0.00200

Alfa

AF:

0.00109

Hom.:

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 submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jun 11, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.067

CADD

Benign

0.056

DEOGEN2

Benign

0.00057

T;T;.;T

LIST_S2

Benign

0.047

.;T;T;T

MetaRNN

Benign

0.052

T;T;T;T

PROVEAN

Benign

2.6

N;.;N;N

Sift

Benign

1.0

T;.;T;T

Sift4G

Benign

1.0

T;T;.;.

Vest4

0.039

gMVP

0.17

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