rs10521881

Variant names:

• chrX-149294697-A-G
• rs10521881

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 0.0613 in 111,668 control chromosomes in the GnomAD database, including 195 homozygotes. There are 2,030 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 0.061 (195 hom., 2030 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0910
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.137 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: 0.0612 AC: 6836 AN: 111614 Hom.: 195 Cov.: 23

Gnomad AFR AF: 0.0935

Gnomad AMI AF: 0.0103

Gnomad AMR AF: 0.0235

Gnomad ASJ AF: 0.0535

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.0576

Gnomad FIN AF: 0.0748

Gnomad MID AF: 0.0167

Gnomad NFE AF: 0.0446

Gnomad OTH AF: 0.0540

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

GnomAD4 genome AF: 0.0613 AC: 6841 AN: 111668 Hom.: 195 Cov.: 23 AF XY: 0.0600 AC XY: 2030 AN XY: 33844

African (AFR) AF: 0.0935 AC: 2873 AN: 30741

American (AMR) AF: 0.0233 AC: 246 AN: 10540

Ashkenazi Jewish (ASJ) AF: 0.0535 AC: 141 AN: 2635

East Asian (EAS) AF: 0.147 AC: 518 AN: 3520

South Asian (SAS) AF: 0.0577 AC: 153 AN: 2651

European-Finnish (FIN) AF: 0.0748 AC: 449 AN: 6005

Middle Eastern (MID) AF: 0.0138 AC: 3 AN: 218

European-Non Finnish (NFE) AF: 0.0445 AC: 2368 AN: 53157

Other (OTH) AF: 0.0546 AC: 83 AN: 1519

Alfa AF: 0.0658 Hom.: 1118

Bravo AF: 0.0606

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.99
DANN	Benign	0.69
PhyloP100		0.091

Splicing

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

Other links and lift over

dbSNP: rs10521881; hg19: chrX-148376227;