rs861508

chrX-141269590-T-CchrX-141269590-T-G

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

The ENST00000662492.1(SPANXA2-OT1):n.102+81753T>C variant causes a intron, non coding transcript 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 0.81 (26045 hom., 26102 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: SPANXA2-OT1 ENST00000662492.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.122

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BS2: High Homozygotes in GnomAd at 26049 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SPANXA2-OT1	ENST00000662492.1	n.102+81753T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.806 AC: 88660 AN: 110053 Hom.: 26049 Cov.: 23 AF XY: 0.805 AC XY: 26052 AN XY: 32377

Gnomad AFR AF: 0.588

Gnomad AMI AF: 0.976

Gnomad AMR AF: 0.811

Gnomad ASJ AF: 0.921

Gnomad EAS AF: 0.718

Gnomad SAS AF: 0.820

Gnomad FIN AF: 0.882

Gnomad MID AF: 0.902

Gnomad NFE AF: 0.917

Gnomad OTH AF: 0.827

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: InbreedingCoeff AF: 0.806 AC: 88705 AN: 110107 Hom.: 26045 Cov.: 23 AF XY: 0.805 AC XY: 26102 AN XY: 32441

Gnomad4 AFR AF: 0.588

Gnomad4 AMR AF: 0.811

Gnomad4 ASJ AF: 0.921

Gnomad4 EAS AF: 0.718

Gnomad4 SAS AF: 0.822

Gnomad4 FIN AF: 0.882

Gnomad4 NFE AF: 0.917

Gnomad4 OTH AF: 0.826

Alfa AF: 0.893 Hom.: 66527

Bravo AF: 0.792

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	1.2

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs861508; hg19: chrX-140363732;