rs7879053

Variant names:

• chrX-138482874-C-T
• rs7879053
• ENST00000418272.1:n.130C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000418272.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAGEA13P	ENST00000418272.1	TSL:6	n.130C>T		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0758 AC: 8431 AN: 111294 Hom.: 789 Cov.: 22

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

African (AFR) AF: 1.00 AC: 2 AN: 2

American (AMR) AF: 0.00 AC: 0 AN: 2

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AF: 0.00 AC: 0 AN: 1

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 3

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 75

Other (OTH) AF: 0.167 AC: 1 AN: 6

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

African (AFR) AF: 0.263 AC: 7976 AN: 30365

American (AMR) AF: 0.0317 AC: 335 AN: 10575

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2638

East Asian (EAS) AF: 0.00 AC: 0 AN: 3515

South Asian (SAS) AF: 0.00114 AC: 3 AN: 2635

European-Finnish (FIN) AF: 0.000329 AC: 2 AN: 6076

Middle Eastern (MID) AF: 0.00465 AC: 1 AN: 215

European-Non Finnish (NFE) AF: 0.000828 AC: 44 AN: 53109

Other (OTH) AF: 0.0582 AC: 89 AN: 1529

Alfa AF: 0.0353 Hom.: 3036

Bravo AF: 0.0881

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.5
DANN	Benign	0.67
PhyloP100		-0.99

Splicing

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

Other links and lift over

dbSNP: rs7879053; hg19: chrX-137565032;