rs10521394

Variant names:

• chrX-80003601-A-G
• rs10521394

Your query was ambiguous. Multiple possible variants found:

• chrX-80003601-A-G
• chrX-80003601-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 0.0571 in 111,144 control chromosomes in the GnomAD database, including 342 homozygotes. There are 2,046 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 0.057 (342 hom., 2046 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.39
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.447 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0570 AC: 6333 AN: 111095 Hom.: 341 Cov.: 23

Gnomad AFR AF: 0.0404

Gnomad AMI AF: 0.0511

Gnomad AMR AF: 0.0632

Gnomad ASJ AF: 0.0201

Gnomad EAS AF: 0.466

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.0949

Gnomad MID AF: 0.0299

Gnomad NFE AF: 0.0333

Gnomad OTH AF: 0.0666

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

GnomAD4 genome AF: 0.0571 AC: 6350 AN: 111144 Hom.: 342 Cov.: 23 AF XY: 0.0611 AC XY: 2046 AN XY: 33498

African (AFR) AF: 0.0409 AC: 1260 AN: 30842

American (AMR) AF: 0.0634 AC: 656 AN: 10350

Ashkenazi Jewish (ASJ) AF: 0.0201 AC: 53 AN: 2635

East Asian (EAS) AF: 0.466 AC: 1615 AN: 3469

South Asian (SAS) AF: 0.112 AC: 302 AN: 2706

European-Finnish (FIN) AF: 0.0949 AC: 561 AN: 5912

Middle Eastern (MID) AF: 0.0374 AC: 8 AN: 214

European-Non Finnish (NFE) AF: 0.0333 AC: 1757 AN: 52811

Other (OTH) AF: 0.0678 AC: 103 AN: 1520

Alfa AF: 0.0429 Hom.: 220

Bravo AF: 0.0622

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.6
DANN	Benign	0.68
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs10521394; hg19: chrX-79259100;