rs10521829

chrX-142801592-A-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;