rs41300301

Variant names:

• chrX-141908886-C-T
• rs41300301
• NM_005462.5:c.*53C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005462.5. 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
	MAGEC1	NM_005462.5	MANE Select	c.*53C>T		3_prime_UTR	Exon 4 of 4	NP_005453.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAGEC1	ENST00000285879.5	TSL:1 MANE Select	c.*53C>T		3_prime_UTR	Exon 4 of 4	ENSP00000285879.4
	MAGEC1	ENST00000406005.2	TSL:1	c.*53C>T		3_prime_UTR	Exon 4 of 4	ENSP00000385500.2

Frequencies

GnomAD3 genomes AF: 0.0857 AC: 9533 AN: 111293 Hom.: 325 Cov.: 23

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

African (AFR) AF: 0.0787 AC: 1776 AN: 22575

American (AMR) AF: 0.0872 AC: 2151 AN: 24663

Ashkenazi Jewish (ASJ) AF: 0.0394 AC: 572 AN: 14527

East Asian (EAS) AF: 0.0473 AC: 1388 AN: 29335

South Asian (SAS) AF: 0.141 AC: 5662 AN: 40242

European-Finnish (FIN) AF: 0.0921 AC: 3365 AN: 36518

Middle Eastern (MID) AF: 0.109 AC: 394 AN: 3628

European-Non Finnish (NFE) AF: 0.108 AC: 79841 AN: 737899

Other (OTH) AF: 0.0930 AC: 3769 AN: 40530

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

African (AFR) AF: 0.0696 AC: 2134 AN: 30678

American (AMR) AF: 0.0668 AC: 704 AN: 10535

Ashkenazi Jewish (ASJ) AF: 0.0348 AC: 92 AN: 2641

East Asian (EAS) AF: 0.0484 AC: 170 AN: 3515

South Asian (SAS) AF: 0.131 AC: 342 AN: 2618

European-Finnish (FIN) AF: 0.0888 AC: 528 AN: 5946

Middle Eastern (MID) AF: 0.0556 AC: 12 AN: 216

European-Non Finnish (NFE) AF: 0.102 AC: 5403 AN: 53008

Other (OTH) AF: 0.0844 AC: 127 AN: 1504

Alfa AF: 0.0999 Hom.: 858

Bravo AF: 0.0817

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.48
DANN	Benign	0.35
PhyloP100		-2.9
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
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: rs41300301; hg19: chrX-140996672; COSMIC: COSV107256692;