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GeneBe

X-51896717-G-A

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_006986.4(MAGED1):c.1062G>A(p.Val354=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000608 in 1,210,702 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 220 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.00039 ( 0 hom., 10 hem., cov: 23)
Exomes 𝑓: 0.00063 ( 0 hom. 210 hem. )

Consequence

MAGED1
NM_006986.4 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.374
Variant links:
Genes affected
MAGED1 (HGNC:6813): (MAGE family member D1) This gene is a member of the melanoma antigen gene (MAGE) family. Most of the genes of this family encode tumor specific antigens that are not expressed in normal adult tissues except testis. Although the protein encoded by this gene shares strong homology with members of the MAGE family, it is expressed in almost all normal adult tissues. This gene has been demonstrated to be involved in the p75 neurotrophin receptor mediated programmed cell death pathway. Three transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant X-51896717-G-A is Benign according to our data. Variant chrX-51896717-G-A is described in ClinVar as [Benign]. Clinvar id is 756007.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-0.374 with no splicing effect.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High Hemizygotes in GnomAd at 10 gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
MAGED1NM_006986.4 linkuse as main transcriptc.1062G>A p.Val354= synonymous_variant 4/13 ENST00000326587.12

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MAGED1ENST00000326587.12 linkuse as main transcriptc.1062G>A p.Val354= synonymous_variant 4/131 NM_006986.4 P2Q9Y5V3-1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.000391
AC:
44
AN:
112404
Hom.:
0
Cov.:
23
AF XY:
0.000289
AC XY:
10
AN XY:
34588
show subpopulations
Gnomad AFR
AF:
0.0000323
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:
0.000323
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000771
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000540
AC:
99
AN:
183347
Hom.:
0
AF XY:
0.000605
AC XY:
41
AN XY:
67821
show subpopulations
Gnomad AFR exome
AF:
0.000152
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00106
Gnomad NFE exome
AF:
0.000928
Gnomad OTH exome
AF:
0.000884
GnomAD4 exome
AF:
0.000630
AC:
692
AN:
1098244
Hom.:
0
Cov.:
32
AF XY:
0.000578
AC XY:
210
AN XY:
363600
show subpopulations
Gnomad4 AFR exome
AF:
0.0000757
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00101
Gnomad4 NFE exome
AF:
0.000753
Gnomad4 OTH exome
AF:
0.000304
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.000391
AC:
44
AN:
112458
Hom.:
0
Cov.:
23
AF XY:
0.000289
AC XY:
10
AN XY:
34652
show subpopulations
Gnomad4 AFR
AF:
0.0000323
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.000323
Gnomad4 NFE
AF:
0.000771
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.000509
Hom.:
4
Bravo
AF:
0.000344
EpiCase
AF:
0.000763
EpiControl
AF:
0.000415

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 submitterclinical testingInvitaeAug 16, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.81
Cadd
Benign
5.3
Dann
Benign
0.66

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.

Other links and lift over

dbSNP: rs138624949; hg19: chrX-51639813; COSMIC: COSV100431934; COSMIC: COSV100431934; API