ENST00000662492.1:n.103-148534T>C

Variant names:

• chrX-141344617-T-C
• rs844970
• ENST00000662492.1:n.103-148534T>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.103-148534T>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 0.62 (15104 hom., 20814 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: SPANXA2-OT1 ENST00000662492.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.355
• Publications: 1 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=-0.86).

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.103-148534T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.623 AC: 69083 AN: 110881 Hom.: 15116 Cov.: 23

Gnomad AFR AF: 0.566

Gnomad AMI AF: 0.630

Gnomad AMR AF: 0.684

Gnomad ASJ AF: 0.653

Gnomad EAS AF: 0.492

Gnomad SAS AF: 0.640

Gnomad FIN AF: 0.698

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.641

Gnomad OTH AF: 0.627

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: 0.623 AC: 69105 AN: 110931 Hom.: 15104 Cov.: 23 AF XY: 0.627 AC XY: 20814 AN XY: 33185

African (AFR) AF: 0.566 AC: 17255 AN: 30506

American (AMR) AF: 0.685 AC: 7168 AN: 10470

Ashkenazi Jewish (ASJ) AF: 0.653 AC: 1722 AN: 2636

East Asian (EAS) AF: 0.492 AC: 1703 AN: 3463

South Asian (SAS) AF: 0.641 AC: 1708 AN: 2666

European-Finnish (FIN) AF: 0.698 AC: 4105 AN: 5880

Middle Eastern (MID) AF: 0.705 AC: 153 AN: 217

European-Non Finnish (NFE) AF: 0.641 AC: 33927 AN: 52910

Other (OTH) AF: 0.623 AC: 939 AN: 1508

Alfa AF: 0.626 Hom.: 21072

Bravo AF: 0.621

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.2
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs844970; hg19: chrX-140438761;