rs10521866

Variant names:

• chrX-147758954-G-A
• rs10521866

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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

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

African (AFR) AF: 0.120 AC: 3664 AN: 30537

American (AMR) AF: 0.0455 AC: 476 AN: 10467

Ashkenazi Jewish (ASJ) AF: 0.0961 AC: 253 AN: 2634

East Asian (EAS) AF: 0.00112 AC: 4 AN: 3558

South Asian (SAS) AF: 0.0831 AC: 219 AN: 2636

European-Finnish (FIN) AF: 0.0428 AC: 254 AN: 5941

Middle Eastern (MID) AF: 0.0755 AC: 16 AN: 212

European-Non Finnish (NFE) AF: 0.0749 AC: 3971 AN: 52984

Other (OTH) AF: 0.0777 AC: 118 AN: 1519

Alfa AF: 0.0798 Hom.: 4065

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
PhyloP100		-0.92

Splicing

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

Other links and lift over

dbSNP: rs10521866; hg19: chrX-146840472;