X-141243572-A-G

Variant names:

• chrX-141243572-A-G
• rs12394263
• ENST00000662492.1:n.102+55735A>G

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000662492.1(SPANXA2-OT1):​n.102+55735A>G variant causes a intron 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 0.045 (92 hom., 12 hem., cov: 1)
  • Failed GnomAD Quality Control
• Consequence: SPANXA2-OT1 ENST00000662492.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0720
• Publications: 0 publications found

Genes affected

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

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SPANXA2-OT1	ENST00000662492.1	n.102+55735A>G		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.0446 AC: 1309 AN: 29331 Hom.: 91 Cov.: 1

Gnomad AFR AF: 0.0193

Gnomad AMI AF: 0.00567

Gnomad AMR AF: 0.0486

Gnomad ASJ AF: 0.0728

Gnomad EAS AF: 0.0146

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.0103

Gnomad MID AF: 0.0278

Gnomad NFE AF: 0.0700

Gnomad OTH AF: 0.0379

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0447 AC: 1312 AN: 29350 Hom.: 92 Cov.: 1 AF XY: 0.00180 AC XY: 12 AN XY: 6682

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.0193 AC: 218 AN: 11287

American (AMR) AF: 0.0498 AC: 123 AN: 2470

Ashkenazi Jewish (ASJ) AF: 0.0728 AC: 49 AN: 673

East Asian (EAS) AF: 0.0146 AC: 9 AN: 615

South Asian (SAS) AF: 0.155 AC: 63 AN: 406

European-Finnish (FIN) AF: 0.0103 AC: 15 AN: 1454

Middle Eastern (MID) AF: 0.0294 AC: 1 AN: 34

European-Non Finnish (NFE) AF: 0.0699 AC: 819 AN: 11713

Other (OTH) AF: 0.0377 AC: 13 AN: 345

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.0867 Hom.: 220

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	4.0
DANN	Benign	0.46
PhyloP100		0.072

Splicing

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

Other links and lift over

dbSNP: rs12394263; hg19: chrX-140337700;