rs1968987

Variant names:

• chrX-141264142-T-A
• rs1968987
• ENST00000257020.7:n.72A>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

Genes affected

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

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000257020.7. 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
	RBMX2P2	ENST00000257020.7	TSL:6	n.72A>T		non_coding_transcript_exon	Exon 1 of 2
	SPANXA2-OT1	ENST00000662492.1		n.102+76305T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.203 AC: 22462 AN: 110829 Hom.: 1750 Cov.: 22

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

African (AFR) AF: 0.275 AC: 4922 AN: 17895

American (AMR) AF: 0.240 AC: 8027 AN: 33438

Ashkenazi Jewish (ASJ) AF: 0.218 AC: 3412 AN: 15651

East Asian (EAS) AF: 0.120 AC: 3025 AN: 25289

South Asian (SAS) AF: 0.195 AC: 9001 AN: 46106

European-Finnish (FIN) AF: 0.204 AC: 7677 AN: 37675

Middle Eastern (MID) AF: 0.0978 AC: 193 AN: 1974

European-Non Finnish (NFE) AF: 0.196 AC: 90291 AN: 459597

Other (OTH) AF: 0.197 AC: 5971 AN: 30270

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

African (AFR) AF: 0.265 AC: 8078 AN: 30454

American (AMR) AF: 0.196 AC: 2027 AN: 10353

Ashkenazi Jewish (ASJ) AF: 0.218 AC: 575 AN: 2638

East Asian (EAS) AF: 0.126 AC: 440 AN: 3484

South Asian (SAS) AF: 0.194 AC: 514 AN: 2647

European-Finnish (FIN) AF: 0.197 AC: 1171 AN: 5957

Middle Eastern (MID) AF: 0.170 AC: 37 AN: 218

European-Non Finnish (NFE) AF: 0.171 AC: 9078 AN: 52967

Other (OTH) AF: 0.188 AC: 282 AN: 1504

Alfa AF: 0.183 Hom.: 1047

Bravo AF: 0.211

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	4.6
DANN	Benign	0.50
PhyloP100		2.3

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1968987;

hg19: chrX-140358278;