X-138482874-C-T

Position:

• chrX-138482874-C-T

Variant summary

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

The ENST00000418272.1(MAGEA13P):​n.130C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0759 in 111,434 control chromosomes in the GnomAD database, including 790 homozygotes. There are 2,238 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 0.076 (790 hom., 2236 hem., cov: 22)
  • Exomes 𝑓: 0.033 (0 hom. 2 hem.)
• Consequence: MAGEA13P ENST00000418272.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.986

Genes affected

MAGEA13P (HGNC:35154): (MAGE family member A13, pseudogene) Predicted to be involved in negative regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.258 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAGEA13P	ENST00000418272.1	n.130C>T		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.0758 AC: 8431 AN: 111294 Hom.: 789 Cov.: 22 AF XY: 0.0663 AC XY: 2222 AN XY: 33524

Gnomad AFR AF: 0.263

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0318

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00114

Gnomad FIN AF: 0.000329

Gnomad MID AF: 0.00847

Gnomad NFE AF: 0.000828

Gnomad OTH AF: 0.0589

GnomAD4 exome AF: 0.0330 AC: 3 AN: 91 Hom.: 0 Cov.: 0 AF XY: 0.0444 AC XY: 2 AN XY: 45

Gnomad4 AFR exome AF: 1.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.167

GnomAD4 genome AF: 0.0759 AC: 8450 AN: 111343 Hom.: 790 Cov.: 22 AF XY: 0.0666 AC XY: 2236 AN XY: 33585

Gnomad4 AFR AF: 0.263

Gnomad4 AMR AF: 0.0317

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00114

Gnomad4 FIN AF: 0.000329

Gnomad4 NFE AF: 0.000828

Gnomad4 OTH AF: 0.0582

Alfa AF: 0.0102 Hom.: 586

Bravo AF: 0.0881

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.5
DANN	Benign	0.67

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs7879053; hg19: chrX-137565032;