rs1595679

Variant names:

• chrX-51822538-G-A
• rs1595679
• ENST00000898271.1:c.-37+19421G>A

Your query was ambiguous. Multiple possible variants found:

• chrX-51822538-G-A
• chrX-51822538-G-C
• chrX-51822538-G-T

Variant summary

Our verdict is Likely benign. The variant received -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
• Publications: 1 publications found

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

Our verdict: Likely_benign. The variant received -4 ACMG points.

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001005332.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAGED1	NM_001005332.2		c.-37+19421G>A		intron	N/A	NP_001005332.1	Q9Y5V3-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAGED1	ENST00000898271.1		c.-37+19421G>A		intron	N/A	ENSP00000568330.1
	MAGED1	ENST00000943445.1		c.-91-11703G>A		intron	N/A	ENSP00000613504.1
	MAGED1	ENST00000939079.1		c.-37+19421G>A		intron	N/A	ENSP00000609138.1

Frequencies

GnomAD3 genomes AF: 0.859 AC: 92911 AN: 108170 Hom.: 28607 Cov.: 21

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

African (AFR) AF: 0.808 AC: 24172 AN: 29909

American (AMR) AF: 0.929 AC: 9285 AN: 9990

Ashkenazi Jewish (ASJ) AF: 0.903 AC: 2353 AN: 2605

East Asian (EAS) AF: 0.963 AC: 3311 AN: 3437

South Asian (SAS) AF: 0.904 AC: 2218 AN: 2454

European-Finnish (FIN) AF: 0.825 AC: 4308 AN: 5222

Middle Eastern (MID) AF: 0.843 AC: 172 AN: 204

European-Non Finnish (NFE) AF: 0.866 AC: 45229 AN: 52253

Other (OTH) AF: 0.880 AC: 1292 AN: 1469

Alfa AF: 0.866 Hom.: 31483

Bravo AF: 0.867

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.86
DANN	Benign	0.42
PhyloP100		-0.86
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1595679; hg19: chrX-51565634;