X-141259689-T-G

Variant names:

• chrX-141259689-T-G
• rs881223
• ENST00000662492.1:n.102+71852T>G

Variant summary

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

The ENST00000662492.1(SPANXA2-OT1):​n.102+71852T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.16 in 111,518 control chromosomes in the GnomAD database, including 1,048 homozygotes. There are 5,230 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 0.16 (1048 hom., 5230 hem., cov: 24)
• Consequence: SPANXA2-OT1 ENST00000662492.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.597

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 (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.179 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.102+71852T>G		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.160 AC: 17858 AN: 111465 Hom.: 1050 Cov.: 24 AF XY: 0.155 AC XY: 5222 AN XY: 33671

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.410

Gnomad AMR AF: 0.172

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.193

Gnomad MID AF: 0.145

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.147

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

GnomAD4 genome AF: 0.160 AC: 17866 AN: 111518 Hom.: 1048 Cov.: 24 AF XY: 0.155 AC XY: 5230 AN XY: 33734

Gnomad4 AFR AF: 0.152

Gnomad4 AMR AF: 0.172

Gnomad4 ASJ AF: 0.152

Gnomad4 EAS AF: 0.127

Gnomad4 SAS AF: 0.193

Gnomad4 FIN AF: 0.193

Gnomad4 NFE AF: 0.157

Gnomad4 OTH AF: 0.145

Alfa AF: 0.0831 Hom.: 390

Bravo AF: 0.162

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.49
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs881223; hg19: chrX-140353820;