chrX-141265726-C-T

Variant names:

• chrX-141265726-C-T
• rs55843102
• ENST00000662492.1:n.102+77889C>T

Variant summary

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

The ENST00000662492.1(SPANXA2-OT1):​n.102+77889C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.173 in 110,652 control chromosomes in the GnomAD database, including 1,229 homozygotes. There are 5,407 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 0.17 (1229 hom., 5407 hem., cov: 23)
• Consequence: SPANXA2-OT1 ENST00000662492.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.42

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=-0.74).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.178 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+77889C>T		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.173 AC: 19131 AN: 110598 Hom.: 1231 Cov.: 23 AF XY: 0.164 AC XY: 5398 AN XY: 32888

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.417

Gnomad AMR AF: 0.185

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.124

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.191

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.161

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

GnomAD4 genome AF: 0.173 AC: 19142 AN: 110652 Hom.: 1229 Cov.: 23 AF XY: 0.164 AC XY: 5407 AN XY: 32952

Gnomad4 AFR AF: 0.169

Gnomad4 AMR AF: 0.185

Gnomad4 ASJ AF: 0.194

Gnomad4 EAS AF: 0.125

Gnomad4 SAS AF: 0.187

Gnomad4 FIN AF: 0.191

Gnomad4 NFE AF: 0.170

Gnomad4 OTH AF: 0.159

Alfa AF: 0.165 Hom.: 949

Bravo AF: 0.178

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	0.83
DANN	Benign	0.95

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs55843102; hg19: chrX-140359868;