rs10521782

Variant names:

• chrX-137143005-A-G
• rs10521782

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 0.199 in 110,967 control chromosomes in the GnomAD database, including 1,781 homozygotes. There are 6,447 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 0.20 (1781 hom., 6447 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.97

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.274 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: 0.199 AC: 22088 AN: 110914 Hom.: 1785 Cov.: 22 AF XY: 0.194 AC XY: 6439 AN XY: 33174

Gnomad AFR AF: 0.0994

Gnomad AMI AF: 0.360

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.162

Gnomad EAS AF: 0.167

Gnomad SAS AF: 0.292

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.277

Gnomad NFE AF: 0.240

Gnomad OTH AF: 0.224

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

GnomAD4 genome AF: 0.199 AC: 22091 AN: 110967 Hom.: 1781 Cov.: 22 AF XY: 0.194 AC XY: 6447 AN XY: 33237

Gnomad4 AFR AF: 0.0993

Gnomad4 AMR AF: 0.273

Gnomad4 ASJ AF: 0.162

Gnomad4 EAS AF: 0.168

Gnomad4 SAS AF: 0.291

Gnomad4 FIN AF: 0.190

Gnomad4 NFE AF: 0.240

Gnomad4 OTH AF: 0.227

Alfa AF: 0.229 Hom.: 4974

Bravo AF: 0.204

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.9
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10521782; hg19: chrX-136225164;