rs10521807

chrX-141743717-A-CchrX-141743717-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 0.185 in 111,288 control chromosomes in the GnomAD database, including 1,671 homozygotes. There are 6,091 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 0.18 (1671 hom., 6091 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.485

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.257 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: 0.185 AC: 20576 AN: 111243 Hom.: 1671 Cov.: 23 AF XY: 0.182 AC XY: 6093 AN XY: 33489

Gnomad AFR AF: 0.0502

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.188

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.0182

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.285

Gnomad MID AF: 0.210

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.196

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

GnomAD4 genome AF: 0.185 AC: 20564 AN: 111288 Hom.: 1671 Cov.: 23 AF XY: 0.182 AC XY: 6091 AN XY: 33544

Gnomad4 AFR AF: 0.0501

Gnomad4 AMR AF: 0.188

Gnomad4 ASJ AF: 0.218

Gnomad4 EAS AF: 0.0179

Gnomad4 SAS AF: 0.199

Gnomad4 FIN AF: 0.285

Gnomad4 NFE AF: 0.261

Gnomad4 OTH AF: 0.192

Alfa AF: 0.223 Hom.: 4463

Bravo AF: 0.173

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
Cadd	Benign	1.6
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: rs10521807; hg19: chrX-140831918;