rs3765272

Variant names:

• chrX-142203079-C-T
• rs3765272
• NM_016249.4:c.909G>A

Variant summary

Our verdict is Likely benign. The variant received -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
• Publications: 16 publications found

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

Our verdict: Likely_benign. The variant received -5 ACMG points.

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016249.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAGEC2	NM_016249.4	MANE Select	c.909G>A	p.Pro303Pro	synonymous	Exon 3 of 3	NP_057333.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAGEC2	ENST00000247452.4	TSL:1 MANE Select	c.909G>A	p.Pro303Pro	synonymous	Exon 3 of 3	ENSP00000354660.2
	ENSG00000288098	ENST00000664519.1		n.300+7295C>T		intron	N/A
	ENSG00000288098	ENST00000842232.1		n.78+7295C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.673 AC: 73898 AN: 109828 Hom.: 17819 Cov.: 22

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

GnomAD2 exomes AF: 0.706 AC: 129342 AN: 183308 AF XY: 0.703

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 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

African (AFR) AF: 0.597 AC: 15769 AN: 26395

American (AMR) AF: 0.756 AC: 26624 AN: 35202

Ashkenazi Jewish (ASJ) AF: 0.733 AC: 14214 AN: 19384

East Asian (EAS) AF: 0.887 AC: 26787 AN: 30206

South Asian (SAS) AF: 0.684 AC: 37053 AN: 54142

European-Finnish (FIN) AF: 0.646 AC: 26171 AN: 40515

Middle Eastern (MID) AF: 0.691 AC: 2859 AN: 4136

European-Non Finnish (NFE) AF: 0.697 AC: 587168 AN: 841953

Other (OTH) AF: 0.705 AC: 32486 AN: 46093

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

African (AFR) AF: 0.603 AC: 18198 AN: 30186

American (AMR) AF: 0.740 AC: 7636 AN: 10325

Ashkenazi Jewish (ASJ) AF: 0.716 AC: 1877 AN: 2621

East Asian (EAS) AF: 0.872 AC: 3000 AN: 3439

South Asian (SAS) AF: 0.685 AC: 1711 AN: 2498

European-Finnish (FIN) AF: 0.636 AC: 3682 AN: 5785

Middle Eastern (MID) AF: 0.687 AC: 145 AN: 211

European-Non Finnish (NFE) AF: 0.688 AC: 36257 AN: 52667

Other (OTH) AF: 0.706 AC: 1047 AN: 1484

Alfa AF: 0.683 Hom.: 15694

Bravo AF: 0.682

EpiCase AF: 0.699

EpiControl AF: 0.702

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	0.30
DANN	Benign	0.40
PhyloP100		-1.9
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: rs3765272; hg19: chrX-141290865; COSMIC: COSV55998525;