ENST00000662492.1:n.102+81021T>C

Variant names:

• chrX-141268858-T-C
• rs845156
• ENST00000662492.1:n.102+81021T>C

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+81021T>C 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 0.90 (31376 hom., 29189 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: SPANXA2-OT1 ENST00000662492.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.56
• 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=-0.88).

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPANXA2-OT1	ENST00000662492.1		n.102+81021T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.896 AC: 98732 AN: 110145 Hom.: 31385 Cov.: 23

Gnomad AFR AF: 0.776

Gnomad AMI AF: 0.994

Gnomad AMR AF: 0.939

Gnomad ASJ AF: 0.956

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.966

Gnomad FIN AF: 0.912

Gnomad MID AF: 0.954

Gnomad NFE AF: 0.940

Gnomad OTH AF: 0.908

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: 0.896 AC: 98780 AN: 110203 Hom.: 31376 Cov.: 23 AF XY: 0.899 AC XY: 29189 AN XY: 32455

African (AFR) AF: 0.776 AC: 23577 AN: 30366

American (AMR) AF: 0.940 AC: 9599 AN: 10217

Ashkenazi Jewish (ASJ) AF: 0.956 AC: 2518 AN: 2635

East Asian (EAS) AF: 0.997 AC: 3477 AN: 3486

South Asian (SAS) AF: 0.968 AC: 2497 AN: 2580

European-Finnish (FIN) AF: 0.912 AC: 5251 AN: 5760

Middle Eastern (MID) AF: 0.949 AC: 206 AN: 217

European-Non Finnish (NFE) AF: 0.940 AC: 49631 AN: 52774

Other (OTH) AF: 0.906 AC: 1348 AN: 1488

Alfa AF: 0.921 Hom.: 117312

Bravo AF: 0.895

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.76
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs845156; hg19: chrX-140363000;