rs10522054

chrX-90093685-C-G

Variant summary

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

The variant allele was found at a frequency of 0.0173 in 107,040 control chromosomes in the GnomAD database, including 37 homozygotes. There are 487 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 0.017 (37 hom., 487 hem., cov: 20)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.73

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0557 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0173 AC: 1846 AN: 107010 Hom.: 35 Cov.: 20 AF XY: 0.0162 AC XY: 486 AN XY: 30020

Gnomad AFR AF: 0.00348

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0592

Gnomad ASJ AF: 0.0108

Gnomad EAS AF: 0.0115

Gnomad SAS AF: 0.0265

Gnomad FIN AF: 0.0160

Gnomad MID AF: 0.00877

Gnomad NFE AF: 0.0178

Gnomad OTH AF: 0.0183

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

GnomAD4 genome AF: 0.0173 AC: 1852 AN: 107040 Hom.: 37 Cov.: 20 AF XY: 0.0162 AC XY: 487 AN XY: 30060

Gnomad4 AFR AF: 0.00348

Gnomad4 AMR AF: 0.0598

Gnomad4 ASJ AF: 0.0108

Gnomad4 EAS AF: 0.0115

Gnomad4 SAS AF: 0.0265

Gnomad4 FIN AF: 0.0160

Gnomad4 NFE AF: 0.0178

Gnomad4 OTH AF: 0.0181

Alfa AF: 0.0173 Hom.: 78

Bravo AF: 0.0202

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.35
Dann	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10522054; hg19: chrX-89348684;