chrX-141908886-C-T

Position:

• chrX-141908886-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005462.5(MAGEC1):​c.*53C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.102 in 1,061,261 control chromosomes in the GnomAD database, including 3,900 homozygotes. There are 32,708 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 0.086 (323 hom., 2703 hem., cov: 23)
  • Exomes 𝑓: 0.10 (3577 hom. 30005 hem.)
• Consequence: MAGEC1 NM_005462.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.92

Genes affected

MAGEC1 (HGNC:6812): (MAGE family member C1) This gene is a member of the melanoma antigen gene (MAGE) family. The proteins of this family are tumor-specific antigens that can be recognized by autologous cytolytic T lymphocytes. This protein contains a large number of unique short repetitive sequences in front of the MAGE-homologous sequence, and therefore is about 800 aa longer than the other MAGE proteins. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.119 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAGEC1	NM_005462.5	c.*53C>T		3_prime_UTR_variant	4/4	ENST00000285879.5
MAGEC1	XM_011531418.3	c.*53C>T		3_prime_UTR_variant	4/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAGEC1	ENST00000285879.5	c.*53C>T		3_prime_UTR_variant	4/4	1	NM_005462.5	P3
MAGEC1	ENST00000406005.2	c.*53C>T		3_prime_UTR_variant	4/4	1		A2

Frequencies

GnomAD3 genomes AF: 0.0857 AC: 9533 AN: 111293 Hom.: 325 Cov.: 23 AF XY: 0.0805 AC XY: 2696 AN XY: 33505

Gnomad AFR AF: 0.0695

Gnomad AMI AF: 0.0278

Gnomad AMR AF: 0.0672

Gnomad ASJ AF: 0.0348

Gnomad EAS AF: 0.0482

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.0888

Gnomad MID AF: 0.0549

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.0855

GnomAD4 exome AF: 0.104 AC: 98918 AN: 949917 Hom.: 3577 Cov.: 17 AF XY: 0.114 AC XY: 30005 AN XY: 263001

Gnomad4 AFR exome AF: 0.0787

Gnomad4 AMR exome AF: 0.0872

Gnomad4 ASJ exome AF: 0.0394

Gnomad4 EAS exome AF: 0.0473

Gnomad4 SAS exome AF: 0.141

Gnomad4 FIN exome AF: 0.0921

Gnomad4 NFE exome AF: 0.108

Gnomad4 OTH exome AF: 0.0930

GnomAD4 genome AF: 0.0856 AC: 9531 AN: 111344 Hom.: 323 Cov.: 23 AF XY: 0.0805 AC XY: 2703 AN XY: 33566

Gnomad4 AFR AF: 0.0696

Gnomad4 AMR AF: 0.0668

Gnomad4 ASJ AF: 0.0348

Gnomad4 EAS AF: 0.0484

Gnomad4 SAS AF: 0.131

Gnomad4 FIN AF: 0.0888

Gnomad4 NFE AF: 0.102

Gnomad4 OTH AF: 0.0844

Alfa AF: 0.0999 Hom.: 858

Bravo AF: 0.0817

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.48
DANN	Benign	0.35
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs41300301; hg19: chrX-140996672;