rs10521829

Variant names:

• chrX-142801592-A-G
• rs10521829

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 0.0916 in 110,349 control chromosomes in the GnomAD database, including 1,064 homozygotes. There are 2,631 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 0.092 (1064 hom., 2631 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.30

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.291 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: 0.0914 AC: 10085 AN: 110294 Hom.: 1061 Cov.: 22 AF XY: 0.0804 AC XY: 2624 AN XY: 32622

Gnomad AFR AF: 0.296

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0503

Gnomad ASJ AF: 0.00798

Gnomad EAS AF: 0.0419

Gnomad SAS AF: 0.0332

Gnomad FIN AF: 0.0140

Gnomad MID AF: 0.0551

Gnomad NFE AF: 0.00368

Gnomad OTH AF: 0.0963

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

GnomAD4 genome AF: 0.0916 AC: 10103 AN: 110349 Hom.: 1064 Cov.: 22 AF XY: 0.0805 AC XY: 2631 AN XY: 32687

Gnomad4 AFR AF: 0.296

Gnomad4 AMR AF: 0.0503

Gnomad4 ASJ AF: 0.00798

Gnomad4 EAS AF: 0.0417

Gnomad4 SAS AF: 0.0333

Gnomad4 FIN AF: 0.0140

Gnomad4 NFE AF: 0.00368

Gnomad4 OTH AF: 0.100

Alfa AF: 0.0187 Hom.: 584

Bravo AF: 0.106

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	10
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10521829; hg19: chrX-141889378;