rs5951081

Variant names:

• chrX-51820684-T-C
• rs5951081
• ENST00000898271.1:c.-37+17567T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001005332.2(MAGED1):​c.-37+17567T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0429 in 111,979 control chromosomes in the GnomAD database, including 120 homozygotes. There are 1,267 hemizygotes in GnomAD. 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 0.043 (120 hom., 1267 hem., cov: 22)
• Consequence: MAGED1 NM_001005332.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.207
• 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0704 is higher than 0.05.

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+17567T>C		intron	N/A	NP_001005332.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAGED1	ENST00000898271.1		c.-37+17567T>C		intron	N/A	ENSP00000568330.1
	MAGED1	ENST00000943445.1		c.-91-13557T>C		intron	N/A	ENSP00000613504.1
	MAGED1	ENST00000939079.1		c.-37+17567T>C		intron	N/A	ENSP00000609138.1

Frequencies

GnomAD3 genomes AF: 0.0429 AC: 4804 AN: 111928 Hom.: 119 Cov.: 22

Gnomad AFR AF: 0.00959

Gnomad AMI AF: 0.0352

Gnomad AMR AF: 0.0172

Gnomad ASJ AF: 0.0494

Gnomad EAS AF: 0.000555

Gnomad SAS AF: 0.0214

Gnomad FIN AF: 0.0364

Gnomad MID AF: 0.0126

Gnomad NFE AF: 0.0723

Gnomad OTH AF: 0.0332

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

GnomAD4 genome AF: 0.0429 AC: 4808 AN: 111979 Hom.: 120 Cov.: 22 AF XY: 0.0371 AC XY: 1267 AN XY: 34157

African (AFR) AF: 0.00957 AC: 296 AN: 30924

American (AMR) AF: 0.0172 AC: 181 AN: 10543

Ashkenazi Jewish (ASJ) AF: 0.0494 AC: 131 AN: 2653

East Asian (EAS) AF: 0.000557 AC: 2 AN: 3592

South Asian (SAS) AF: 0.0229 AC: 61 AN: 2658

European-Finnish (FIN) AF: 0.0364 AC: 221 AN: 6067

Middle Eastern (MID) AF: 0.00917 AC: 2 AN: 218

European-Non Finnish (NFE) AF: 0.0723 AC: 3840 AN: 53118

Other (OTH) AF: 0.0328 AC: 50 AN: 1525

Alfa AF: 0.0548 Hom.: 319

Bravo AF: 0.0390

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	6.3
DANN	Benign	0.94
PhyloP100		0.21
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: rs5951081; hg19: chrX-51563780;