rs3765272

Positions:

• chrX-142203079-C-T

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_Strong BP7

The NM_016249.4(MAGEC2):​c.909G>A​(p.Pro303Pro) variant causes a synonymous 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 0.67 (17808 hom., 21588 hem., cov: 22)
  • Exomes 𝑓: 0.70 (181549 hom. 254022 hem.)
  • Failed GnomAD Quality Control
• Consequence: MAGEC2 NM_016249.4 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.85

Genes affected

MAGEC2 (HGNC:13574): (MAGE family member C2) This gene is a member of the MAGEC gene family. It is not expressed in normal tissues, except for testis, and is expressed in tumors of various histological types. This gene and the other MAGEC genes are clustered on chromosome Xq26-q27. [provided by RefSeq, Oct 2009]

ENSG00000288098 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -5 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BP7: Synonymous conserved (PhyloP=-1.85 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAGEC2	NM_016249.4	c.909G>A	p.Pro303Pro	synonymous_variant	3/3	ENST00000247452.4	NP_057333.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAGEC2	ENST00000247452.4	c.909G>A	p.Pro303Pro	synonymous_variant	3/3	1	NM_016249.4	ENSP00000354660.2
ENSG00000288098	ENST00000664519.1	n.300+7295C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.673 AC: 73898 AN: 109828 Hom.: 17819 Cov.: 22 AF XY: 0.671 AC XY: 21557 AN XY: 32112

Gnomad AFR AF: 0.603

Gnomad AMI AF: 0.542

Gnomad AMR AF: 0.740

Gnomad ASJ AF: 0.716

Gnomad EAS AF: 0.872

Gnomad SAS AF: 0.685

Gnomad FIN AF: 0.636

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.688

Gnomad OTH AF: 0.705

GnomAD3 exomes AF: 0.706 AC: 129342 AN: 183308 Hom.: 29263 AF XY: 0.703 AC XY: 47650 AN XY: 67756

Gnomad AFR exome AF: 0.600

Gnomad AMR exome AF: 0.757

Gnomad ASJ exome AF: 0.731

Gnomad EAS exome AF: 0.869

Gnomad SAS exome AF: 0.696

Gnomad FIN exome AF: 0.640

Gnomad NFE exome AF: 0.691

Gnomad OTH exome AF: 0.701

GnomAD4 exome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.700 AC: 769131 AN: 1098026 Hom.: 181549 Cov.: 47 AF XY: 0.699 AC XY: 254022 AN XY: 363420

Gnomad4 AFR exome AF: 0.597

Gnomad4 AMR exome AF: 0.756

Gnomad4 ASJ exome AF: 0.733

Gnomad4 EAS exome AF: 0.887

Gnomad4 SAS exome AF: 0.684

Gnomad4 FIN exome AF: 0.646

Gnomad4 NFE exome AF: 0.697

Gnomad4 OTH exome AF: 0.705

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.673 AC: 73912 AN: 109878 Hom.: 17808 Cov.: 22 AF XY: 0.671 AC XY: 21588 AN XY: 32172

Gnomad4 AFR AF: 0.603

Gnomad4 AMR AF: 0.740

Gnomad4 ASJ AF: 0.716

Gnomad4 EAS AF: 0.872

Gnomad4 SAS AF: 0.685

Gnomad4 FIN AF: 0.636

Gnomad4 NFE AF: 0.688

Gnomad4 OTH AF: 0.706

Alfa AF: 0.683 Hom.: 14439

Bravo AF: 0.682

EpiCase AF: 0.699

EpiControl AF: 0.702

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	0.30
DANN	Benign	0.40

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: rs3765272; hg19: chrX-141290865; COSMIC: COSV55998525;