rs10521394

chrX-80003601-A-GchrX-80003601-A-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0570 AC: 6333 AN: 111095 Hom.: 341 Cov.: 23 AF XY: 0.0609 AC XY: 2035 AN XY: 33439

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

Gnomad4 AFR AF: 0.0409

Gnomad4 AMR AF: 0.0634

Gnomad4 ASJ AF: 0.0201

Gnomad4 EAS AF: 0.466

Gnomad4 SAS AF: 0.112

Gnomad4 FIN AF: 0.0949

Gnomad4 NFE AF: 0.0333

Gnomad4 OTH AF: 0.0678

Alfa AF: 0.0429 Hom.: 220

Bravo AF: 0.0622

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	4.6
Dann	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10521394; hg19: chrX-79259100;