X-141278334-A-G

Variant names:

• chrX-141278334-A-G
• rs845165
• ENST00000662492.1:n.102+90497A>G

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+90497A>G 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 0.64 (16779 hom., 20770 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: SPANXA2-OT1 ENST00000662492.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.951
• 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=-0.85).

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+90497A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.643 AC: 70931 AN: 110258 Hom.: 16785 Cov.: 23

Gnomad AFR AF: 0.471

Gnomad AMI AF: 0.559

Gnomad AMR AF: 0.626

Gnomad ASJ AF: 0.704

Gnomad EAS AF: 0.573

Gnomad SAS AF: 0.644

Gnomad FIN AF: 0.674

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.744

Gnomad OTH AF: 0.672

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: 0.643 AC: 70970 AN: 110313 Hom.: 16779 Cov.: 23 AF XY: 0.638 AC XY: 20770 AN XY: 32571

African (AFR) AF: 0.471 AC: 14297 AN: 30364

American (AMR) AF: 0.627 AC: 6462 AN: 10314

Ashkenazi Jewish (ASJ) AF: 0.704 AC: 1851 AN: 2631

East Asian (EAS) AF: 0.573 AC: 1972 AN: 3444

South Asian (SAS) AF: 0.647 AC: 1665 AN: 2575

European-Finnish (FIN) AF: 0.674 AC: 3911 AN: 5805

Middle Eastern (MID) AF: 0.728 AC: 158 AN: 217

European-Non Finnish (NFE) AF: 0.744 AC: 39274 AN: 52800

Other (OTH) AF: 0.673 AC: 1011 AN: 1503

Alfa AF: 0.699 Hom.: 38269

Bravo AF: 0.631

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	7.2
PhyloP100		0.95

Splicing

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

Other links and lift over

dbSNP: rs845165; hg19: chrX-140372474;