rs55843102

Positions:

• chrX-141265726-C-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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SPANXA2-OT1	ENST00000662492.1	n.102+77889C>T		intron_variant, non_coding_transcript_variant

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;