X-141352691-A-G

Variant names:

• chrX-141352691-A-G
• rs844963
• ENST00000662492.1:n.103-140460A>G

Variant summary

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

The ENST00000662492.1(SPANXA2-OT1):​n.103-140460A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.288 in 110,660 control chromosomes in the GnomAD database, including 3,667 homozygotes. There are 9,047 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 0.29 (3667 hom., 9047 hem., cov: 23)
• Consequence: SPANXA2-OT1 ENST00000662492.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.384

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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.392 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.103-140460A>G		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.288 AC: 31816 AN: 110604 Hom.: 3667 Cov.: 23 AF XY: 0.275 AC XY: 9025 AN XY: 32878

Gnomad AFR AF: 0.398

Gnomad AMI AF: 0.135

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.338

Gnomad EAS AF: 0.0187

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.295

Gnomad MID AF: 0.309

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.304

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

GnomAD4 genome AF: 0.288 AC: 31835 AN: 110660 Hom.: 3667 Cov.: 23 AF XY: 0.275 AC XY: 9047 AN XY: 32944

Gnomad4 AFR AF: 0.398

Gnomad4 AMR AF: 0.194

Gnomad4 ASJ AF: 0.338

Gnomad4 EAS AF: 0.0190

Gnomad4 SAS AF: 0.121

Gnomad4 FIN AF: 0.295

Gnomad4 NFE AF: 0.267

Gnomad4 OTH AF: 0.301

Alfa AF: 0.298 Hom.: 1977

Bravo AF: 0.287

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs844963; hg19: chrX-140446840;