rs10522054

Variant names:

• chrX-90093685-C-G
• rs10522054

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0173 AC: 1846 AN: 107010 Hom.: 35 Cov.: 20

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

African (AFR) AF: 0.00348 AC: 102 AN: 29333

American (AMR) AF: 0.0598 AC: 578 AN: 9669

Ashkenazi Jewish (ASJ) AF: 0.0108 AC: 28 AN: 2600

East Asian (EAS) AF: 0.0115 AC: 38 AN: 3302

South Asian (SAS) AF: 0.0265 AC: 63 AN: 2373

European-Finnish (FIN) AF: 0.0160 AC: 83 AN: 5199

Middle Eastern (MID) AF: 0.00966 AC: 2 AN: 207

European-Non Finnish (NFE) AF: 0.0178 AC: 932 AN: 52246

Other (OTH) AF: 0.0181 AC: 26 AN: 1433

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
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs10522054; hg19: chrX-89348684;