X-141356084-A-G

Variant names:

• chrX-141356084-A-G
• rs844956
• ENST00000662492.1:n.103-137067A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000662492.1(SPANXA2-OT1):​n.103-137067A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.235 in 110,529 control chromosomes in the GnomAD database, including 2,673 homozygotes. There are 7,461 hemizygotes in GnomAD. 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 0.24 (2673 hom., 7461 hem., cov: 22)
• Consequence: SPANXA2-OT1 ENST00000662492.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0390

Genes affected

SPANXA2-OT1 (HGNC:31683): (SPANXA2 overlapping transcript 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (Cadd=2.272).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.313 is higher than 0.05.

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.103-137067A>G		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.235 AC: 26005 AN: 110474 Hom.: 2675 Cov.: 22 AF XY: 0.227 AC XY: 7448 AN XY: 32766

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.354

Gnomad EAS AF: 0.0172

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.328

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.317

Gnomad OTH AF: 0.265

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.235 AC: 26009 AN: 110529 Hom.: 2673 Cov.: 22 AF XY: 0.227 AC XY: 7461 AN XY: 32831

Gnomad4 AFR AF: 0.119

Gnomad4 AMR AF: 0.174

Gnomad4 ASJ AF: 0.354

Gnomad4 EAS AF: 0.0175

Gnomad4 SAS AF: 0.135

Gnomad4 FIN AF: 0.328

Gnomad4 NFE AF: 0.317

Gnomad4 OTH AF: 0.263

Alfa AF: 0.286 Hom.: 9805

Bravo AF: 0.220

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
CADD	Benign	2.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs844956; hg19: -;