rs844970

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).

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.103-148534T>C		intron_variant	Intron 2 of 5

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 v4.3

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;