rs10522028

Variant names:

• chrX-34771573-T-A
• rs10522028

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 0.0692 in 110,676 control chromosomes in the GnomAD database, including 408 homozygotes. There are 1,945 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 0.069 (408 hom., 1945 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.42
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.175 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: 0.0692 AC: 7650 AN: 110624 Hom.: 408 Cov.: 22

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.00146

Gnomad AMR AF: 0.0367

Gnomad ASJ AF: 0.0310

Gnomad EAS AF: 0.000570

Gnomad SAS AF: 0.0170

Gnomad FIN AF: 0.0124

Gnomad MID AF: 0.0636

Gnomad NFE AF: 0.0295

Gnomad OTH AF: 0.0627

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

GnomAD4 genome AF: 0.0692 AC: 7662 AN: 110676 Hom.: 408 Cov.: 22 AF XY: 0.0590 AC XY: 1945 AN XY: 32984

African (AFR) AF: 0.179 AC: 5405 AN: 30275

American (AMR) AF: 0.0367 AC: 381 AN: 10384

Ashkenazi Jewish (ASJ) AF: 0.0310 AC: 82 AN: 2647

East Asian (EAS) AF: 0.000572 AC: 2 AN: 3496

South Asian (SAS) AF: 0.0174 AC: 45 AN: 2583

European-Finnish (FIN) AF: 0.0124 AC: 74 AN: 5983

Middle Eastern (MID) AF: 0.0744 AC: 16 AN: 215

European-Non Finnish (NFE) AF: 0.0295 AC: 1563 AN: 52906

Other (OTH) AF: 0.0619 AC: 93 AN: 1503

Alfa AF: 0.0559 Hom.: 279

Bravo AF: 0.0811

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	5.2
DANN	Benign	0.87
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs10522028; hg19: chrX-34789690;