rs10521782

Variant names:

• chrX-137143005-A-G
• rs10521782

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 0.199 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
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• 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

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

African (AFR) AF: 0.0993 AC: 3042 AN: 30644

American (AMR) AF: 0.273 AC: 2856 AN: 10447

Ashkenazi Jewish (ASJ) AF: 0.162 AC: 424 AN: 2624

East Asian (EAS) AF: 0.168 AC: 593 AN: 3521

South Asian (SAS) AF: 0.291 AC: 759 AN: 2611

European-Finnish (FIN) AF: 0.190 AC: 1129 AN: 5950

Middle Eastern (MID) AF: 0.274 AC: 59 AN: 215

European-Non Finnish (NFE) AF: 0.240 AC: 12642 AN: 52767

Other (OTH) AF: 0.227 AC: 344 AN: 1513

Alfa AF: 0.224 Hom.: 7063

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
PhyloP100		2.0

Splicing

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

Other links and lift over

dbSNP: rs10521782; hg19: chrX-136225164;