X-141243587-C-G

Variant names:

• chrX-141243587-C-G
• rs56315408
• ENST00000662492.1:n.102+55750C>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+55750C>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 0.0023 (4 hom., 6 hem., cov: 1)
  • Failed GnomAD Quality Control
• Consequence: SPANXA2-OT1 ENST00000662492.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.15
• 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=-1.0).

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+55750C>G		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.00229 AC: 83 AN: 36282 Hom.: 4 Cov.: 1

Gnomad AFR AF: 0.00248

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00316

Gnomad ASJ AF: 0.00115

Gnomad EAS AF: 0.00820

Gnomad SAS AF: 0.00511

Gnomad FIN AF: 0.000624

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00185

Gnomad OTH AF: 0.00491

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: 0.00229 AC: 83 AN: 36306 Hom.: 4 Cov.: 1 AF XY: 0.000755 AC XY: 6 AN XY: 7948

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

African (AFR) AF: 0.00247 AC: 32 AN: 12930

American (AMR) AF: 0.00315 AC: 10 AN: 3172

Ashkenazi Jewish (ASJ) AF: 0.00115 AC: 1 AN: 868

East Asian (EAS) AF: 0.00822 AC: 5 AN: 608

South Asian (SAS) AF: 0.00514 AC: 3 AN: 584

European-Finnish (FIN) AF: 0.000624 AC: 1 AN: 1603

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 43

European-Non Finnish (NFE) AF: 0.00185 AC: 29 AN: 15694

Other (OTH) AF: 0.00489 AC: 2 AN: 409

⚠️ 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: 0.309 Hom.: 2041

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.59
DANN	Benign	0.38
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs56315408; hg19: chrX-140337715;