X-51822538-G-A

Position:

• chrX-51822538-G-A

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001005332.2(MAGED1):​c.-37+19421G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.86 (28609 hom., 26425 hem., cov: 21)
  • Failed GnomAD Quality Control
• Consequence: MAGED1 NM_001005332.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.858

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]

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAGED1	NM_001005332.2	c.-37+19421G>A		intron_variant			NP_001005332.1
MAGED1	XM_011530835.3	c.-37+3130G>A		intron_variant			XP_011529137.1
MAGED1	XM_047442676.1	c.-30523+19421G>A		intron_variant			XP_047298632.1
MAGED1	XM_047442677.1	c.-111+19421G>A		intron_variant			XP_047298633.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAGED1	ENST00000375772.7	c.-37+19421G>A		intron_variant		5		ENSP00000364927	P2

Frequencies

GnomAD3 genomes AF: 0.859 AC: 92911 AN: 108170 Hom.: 28607 Cov.: 21 AF XY: 0.863 AC XY: 26373 AN XY: 30554

Gnomad AFR AF: 0.808

Gnomad AMI AF: 0.920

Gnomad AMR AF: 0.929

Gnomad ASJ AF: 0.903

Gnomad EAS AF: 0.963

Gnomad SAS AF: 0.903

Gnomad FIN AF: 0.825

Gnomad MID AF: 0.839

Gnomad NFE AF: 0.866

Gnomad OTH AF: 0.878

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.859 AC: 92961 AN: 108218 Hom.: 28609 Cov.: 21 AF XY: 0.863 AC XY: 26425 AN XY: 30612

Gnomad4 AFR AF: 0.808

Gnomad4 AMR AF: 0.929

Gnomad4 ASJ AF: 0.903

Gnomad4 EAS AF: 0.963

Gnomad4 SAS AF: 0.904

Gnomad4 FIN AF: 0.825

Gnomad4 NFE AF: 0.866

Gnomad4 OTH AF: 0.880

Alfa AF: 0.866 Hom.: 19611

Bravo AF: 0.867

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.86
DANN	Benign	0.42

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

Other links and lift over

dbSNP: rs1595679; hg19: chrX-51565634;