rs10521918

Variant names:

• chrX-20765081-A-G
• rs10521918

Your query was ambiguous. Multiple possible variants found:

• chrX-20765081-A-G
• chrX-20765081-A-T

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 0.0697 in 111,350 control chromosomes in the GnomAD database, including 332 homozygotes. There are 2,066 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 0.070 (332 hom., 2066 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0170
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.156 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: 0.0697 AC: 7757 AN: 111298 Hom.: 333 Cov.: 23

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.0839

Gnomad AMR AF: 0.0482

Gnomad ASJ AF: 0.0444

Gnomad EAS AF: 0.0139

Gnomad SAS AF: 0.0109

Gnomad FIN AF: 0.0193

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0360

Gnomad OTH AF: 0.0628

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

GnomAD4 genome AF: 0.0697 AC: 7760 AN: 111350 Hom.: 332 Cov.: 23 AF XY: 0.0615 AC XY: 2066 AN XY: 33598

African (AFR) AF: 0.159 AC: 4873 AN: 30560

American (AMR) AF: 0.0482 AC: 505 AN: 10484

Ashkenazi Jewish (ASJ) AF: 0.0444 AC: 118 AN: 2655

East Asian (EAS) AF: 0.0139 AC: 49 AN: 3520

South Asian (SAS) AF: 0.0110 AC: 29 AN: 2643

European-Finnish (FIN) AF: 0.0193 AC: 117 AN: 6062

Middle Eastern (MID) AF: 0.0463 AC: 10 AN: 216

European-Non Finnish (NFE) AF: 0.0360 AC: 1906 AN: 52999

Other (OTH) AF: 0.0627 AC: 96 AN: 1532

Alfa AF: 0.0509 Hom.: 2182

Bravo AF: 0.0794

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.95
DANN	Benign	0.58
PhyloP100		-0.017

Splicing

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

Other links and lift over

dbSNP: rs10521918; hg19: chrX-20783199;