chrX-141264142-T-A

Position:

• chrX-141264142-T-A

Variant summary

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

The ENST00000257020.7(RBMX2P2):​n.72A>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 0.199 in 778,782 control chromosomes in the GnomAD database, including 10,890 homozygotes. There are 50,529 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 0.20 (1747 hom., 6398 hem., cov: 22)
  • Exomes 𝑓: 0.20 (9143 hom. 44131 hem.)
• Consequence: RBMX2P2 ENST00000257020.7 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.29

Genes affected

RBMX2P2 (HGNC:39924): (RBMX2 pseudogene 2)

SPANXA2-OT1 (HGNC:31683): (SPANXA2 overlapping transcript 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.58).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.26 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RBMX2P2		n.141264142T>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RBMX2P2	ENST00000257020.7	n.72A>T		non_coding_transcript_exon_variant	1/2	6
SPANXA2-OT1	ENST00000662492.1	n.102+76305T>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.203 AC: 22462 AN: 110829 Hom.: 1750 Cov.: 22 AF XY: 0.193 AC XY: 6384 AN XY: 33117

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.412

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.190

GnomAD4 exome AF: 0.198 AC: 132519 AN: 667895 Hom.: 9143 Cov.: 14 AF XY: 0.205 AC XY: 44131 AN XY: 214883

Gnomad4 AFR exome AF: 0.275

Gnomad4 AMR exome AF: 0.240

Gnomad4 ASJ exome AF: 0.218

Gnomad4 EAS exome AF: 0.120

Gnomad4 SAS exome AF: 0.195

Gnomad4 FIN exome AF: 0.204

Gnomad4 NFE exome AF: 0.196

Gnomad4 OTH exome AF: 0.197

GnomAD4 genome AF: 0.203 AC: 22476 AN: 110887 Hom.: 1747 Cov.: 22 AF XY: 0.193 AC XY: 6398 AN XY: 33185

Gnomad4 AFR AF: 0.265

Gnomad4 AMR AF: 0.196

Gnomad4 ASJ AF: 0.218

Gnomad4 EAS AF: 0.126

Gnomad4 SAS AF: 0.194

Gnomad4 FIN AF: 0.197

Gnomad4 NFE AF: 0.171

Gnomad4 OTH AF: 0.188

Alfa AF: 0.183 Hom.: 1047

Bravo AF: 0.211

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	4.6
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1968987; hg19: chrX-140358278;