rs10521807

Variant names:

• chrX-141743717-A-C
• rs10521807

Your query was ambiguous. Multiple possible variants found:

• chrX-141743717-A-C
• chrX-141743717-A-T

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 0.185 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
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.185 AC: 20576 AN: 111243 Hom.: 1671 Cov.: 23

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

African (AFR) AF: 0.0501 AC: 1549 AN: 30935

American (AMR) AF: 0.188 AC: 1954 AN: 10371

Ashkenazi Jewish (ASJ) AF: 0.218 AC: 575 AN: 2638

East Asian (EAS) AF: 0.0179 AC: 64 AN: 3566

South Asian (SAS) AF: 0.199 AC: 537 AN: 2696

European-Finnish (FIN) AF: 0.285 AC: 1671 AN: 5869

Middle Eastern (MID) AF: 0.217 AC: 46 AN: 212

European-Non Finnish (NFE) AF: 0.261 AC: 13766 AN: 52808

Other (OTH) AF: 0.192 AC: 291 AN: 1515

Alfa AF: 0.225 Hom.: 5375

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
PhyloP100		0.48

Splicing

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

Other links and lift over

dbSNP: rs10521807; hg19: chrX-140831918;