ENST00000662492.1:n.102+81753T>C

Variant names:

• chrX-141269590-T-C
• rs861508
• ENST00000662492.1:n.102+81753T>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+81753T>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 0.81 (26045 hom., 26102 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: SPANXA2-OT1 ENST00000662492.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.122
• Publications: 2 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=-0.92).

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPANXA2-OT1	ENST00000662492.1		n.102+81753T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.806 AC: 88660 AN: 110053 Hom.: 26049 Cov.: 23

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

African (AFR) AF: 0.588 AC: 17814 AN: 30301

American (AMR) AF: 0.811 AC: 8352 AN: 10296

Ashkenazi Jewish (ASJ) AF: 0.921 AC: 2416 AN: 2623

East Asian (EAS) AF: 0.718 AC: 2464 AN: 3430

South Asian (SAS) AF: 0.822 AC: 2120 AN: 2579

European-Finnish (FIN) AF: 0.882 AC: 5120 AN: 5802

Middle Eastern (MID) AF: 0.897 AC: 192 AN: 214

European-Non Finnish (NFE) AF: 0.917 AC: 48319 AN: 52675

Other (OTH) AF: 0.826 AC: 1245 AN: 1508

Alfa AF: 0.879 Hom.: 106805

Bravo AF: 0.792

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.2
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs861508; hg19: chrX-140363732;