rs10521355

Variant names:

• chrX-76228401-C-A
• rs10521355

Your query was ambiguous. Multiple possible variants found:

• chrX-76228401-C-A
• chrX-76228401-C-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 0.174 in 111,482 control chromosomes in the GnomAD database, including 3,589 homozygotes. There are 5,404 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 0.17 (3589 hom., 5404 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0190
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.554 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: 0.173 AC: 19301 AN: 111427 Hom.: 3583 Cov.: 23

Gnomad AFR AF: 0.561

Gnomad AMI AF: 0.0234

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.0215

Gnomad EAS AF: 0.0410

Gnomad SAS AF: 0.00921

Gnomad FIN AF: 0.0271

Gnomad MID AF: 0.0753

Gnomad NFE AF: 0.0108

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.174 AC: 19350 AN: 111482 Hom.: 3589 Cov.: 23 AF XY: 0.160 AC XY: 5404 AN XY: 33710

African (AFR) AF: 0.561 AC: 17071 AN: 30418

American (AMR) AF: 0.103 AC: 1076 AN: 10476

Ashkenazi Jewish (ASJ) AF: 0.0215 AC: 57 AN: 2653

East Asian (EAS) AF: 0.0411 AC: 146 AN: 3550

South Asian (SAS) AF: 0.00849 AC: 23 AN: 2708

European-Finnish (FIN) AF: 0.0271 AC: 164 AN: 6057

Middle Eastern (MID) AF: 0.0826 AC: 18 AN: 218

European-Non Finnish (NFE) AF: 0.0108 AC: 573 AN: 53195

Other (OTH) AF: 0.135 AC: 206 AN: 1522

Alfa AF: 0.00779 Hom.: 40

Bravo AF: 0.198

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.93
DANN	Benign	0.36
PhyloP100		0.019

Splicing

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

Other links and lift over

dbSNP: rs10521355; hg19: chrX-75448800;