rs10521866

Variant names:

• chrX-147758954-G-A
• rs10521866

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 0.0808 in 111,174 control chromosomes in the GnomAD database, including 299 homozygotes. There are 2,509 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 0.081 (299 hom., 2509 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.921

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.117 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: 0.0808 AC: 8977 AN: 111123 Hom.: 298 Cov.: 22 AF XY: 0.0748 AC XY: 2499 AN XY: 33389

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.0175

Gnomad AMR AF: 0.0456

Gnomad ASJ AF: 0.0961

Gnomad EAS AF: 0.00112

Gnomad SAS AF: 0.0847

Gnomad FIN AF: 0.0428

Gnomad MID AF: 0.0776

Gnomad NFE AF: 0.0750

Gnomad OTH AF: 0.0732

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

GnomAD4 genome AF: 0.0808 AC: 8987 AN: 111174 Hom.: 299 Cov.: 22 AF XY: 0.0750 AC XY: 2509 AN XY: 33450

Gnomad4 AFR AF: 0.120

Gnomad4 AMR AF: 0.0455

Gnomad4 ASJ AF: 0.0961

Gnomad4 EAS AF: 0.00112

Gnomad4 SAS AF: 0.0831

Gnomad4 FIN AF: 0.0428

Gnomad4 NFE AF: 0.0749

Gnomad4 OTH AF: 0.0777

Alfa AF: 0.0766 Hom.: 2919

Bravo AF: 0.0798

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.15
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10521866; hg19: chrX-146840472;