rs371038613

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_001005333.2(MAGED1):​c.206C>A​(p.Pro69Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000969 in 1,031,651 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 12/17 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 20)
Exomes 𝑓: 9.7e-7 ( 0 hom. 1 hem. )

Consequence

MAGED1
NM_001005333.2 missense

Scores

1
13

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.534
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 Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.06078756).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
MAGED1NM_006986.4 linkc.46-266C>A intron_variant Intron 2 of 12 ENST00000326587.12 NP_008917.3 Q9Y5V3-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MAGED1ENST00000326587.12 linkc.46-266C>A intron_variant Intron 2 of 12 1 NM_006986.4 ENSP00000325333.8 Q9Y5V3-1

Frequencies

GnomAD3 genomes
Cov.:
20
GnomAD4 exome
AF:
9.69e-7
AC:
1
AN:
1031651
Hom.:
0
Cov.:
32
AF XY:
0.00000301
AC XY:
1
AN XY:
332723
show subpopulations
Gnomad4 AFR exome
AF:
0.00
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:
0.00
Gnomad4 NFE exome
AF:
0.00000123
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
20

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
-0.57
T
BayesDel_noAF
Benign
-1.1
CADD
Benign
1.5
DANN
Benign
0.60
FATHMM_MKL
Benign
0.025
N
LIST_S2
Benign
0.33
T
M_CAP
Benign
0.018
T
MetaRNN
Benign
0.061
T
MetaSVM
Benign
-1.1
T
PrimateAI
Benign
0.28
T
PROVEAN
Benign
-0.12
N
REVEL
Benign
0.046
Sift
Benign
0.28
T
Sift4G
Uncertain
0.025
D
Polyphen
0.10
B
Vest4
0.15
MutPred
0.14
Loss of glycosylation at P69 (P = 0.0207);
MVP
0.082
MPC
0.072
ClinPred
0.068
T
GERP RS
-1.9
gMVP
0.14

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

No publications associated with this variant yet.

Other links and lift over

hg19: chrX-51637883; API