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).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000662492.1. 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
	SPANXA2-OT1	ENST00000662492.1		n.102+55735A>G		intron	N/A

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), 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 v4.9

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

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

Other links and lift over

dbSNP: rs12394263;

hg19: chrX-140337700;