rs10521829

Variant names:

• chrX-142801592-A-G
• rs10521829

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 0.0916 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
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• 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

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

African (AFR) AF: 0.296 AC: 8890 AN: 30051

American (AMR) AF: 0.0503 AC: 519 AN: 10325

Ashkenazi Jewish (ASJ) AF: 0.00798 AC: 21 AN: 2632

East Asian (EAS) AF: 0.0417 AC: 146 AN: 3499

South Asian (SAS) AF: 0.0333 AC: 87 AN: 2613

European-Finnish (FIN) AF: 0.0140 AC: 82 AN: 5839

Middle Eastern (MID) AF: 0.0605 AC: 13 AN: 215

European-Non Finnish (NFE) AF: 0.00368 AC: 195 AN: 52997

Other (OTH) AF: 0.100 AC: 150 AN: 1493

Alfa AF: 0.0348 Hom.: 1573

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
PhyloP100		2.3

Splicing

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

Other links and lift over

dbSNP: rs10521829; hg19: chrX-141889378;