rs10521369

Positions:

• chrX-84528171-A-G
• chrX-84528171-A-T

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 0.507 in 109,268 control chromosomes in the GnomAD database, including 11,091 homozygotes. There are 16,070 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 0.51 (11091 hom., 16070 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.319

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.609 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: 0.507 AC: 55361 AN: 109217 Hom.: 11092 Cov.: 22 AF XY: 0.505 AC XY: 16045 AN XY: 31769

Gnomad AFR AF: 0.251

Gnomad AMI AF: 0.659

Gnomad AMR AF: 0.617

Gnomad ASJ AF: 0.691

Gnomad EAS AF: 0.438

Gnomad SAS AF: 0.623

Gnomad FIN AF: 0.561

Gnomad MID AF: 0.626

Gnomad NFE AF: 0.614

Gnomad OTH AF: 0.536

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

GnomAD4 genome AF: 0.507 AC: 55380 AN: 109268 Hom.: 11091 Cov.: 22 AF XY: 0.505 AC XY: 16070 AN XY: 31830

Gnomad4 AFR AF: 0.251

Gnomad4 AMR AF: 0.617

Gnomad4 ASJ AF: 0.691

Gnomad4 EAS AF: 0.439

Gnomad4 SAS AF: 0.626

Gnomad4 FIN AF: 0.561

Gnomad4 NFE AF: 0.614

Gnomad4 OTH AF: 0.540

Alfa AF: 0.548 Hom.: 4113

Bravo AF: 0.502

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.9
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10521369; hg19: chrX-83783179;