rs725886

Variant names:

• chrX-111501933-C-A
• rs725886

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 0.19 in 111,062 control chromosomes in the GnomAD database, including 4,777 homozygotes. There are 5,767 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 0.19 (4777 hom., 5767 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0400

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.639 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: 0.190 AC: 21110 AN: 111019 Hom.: 4774 Cov.: 23 AF XY: 0.172 AC XY: 5729 AN XY: 33261

Gnomad AFR AF: 0.647

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0825

Gnomad ASJ AF: 0.00947

Gnomad EAS AF: 0.000559

Gnomad SAS AF: 0.00604

Gnomad FIN AF: 0.00101

Gnomad MID AF: 0.0681

Gnomad NFE AF: 0.00707

Gnomad OTH AF: 0.146

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

GnomAD4 genome AF: 0.190 AC: 21156 AN: 111062 Hom.: 4777 Cov.: 23 AF XY: 0.173 AC XY: 5767 AN XY: 33314

Gnomad4 AFR AF: 0.647

Gnomad4 AMR AF: 0.0823

Gnomad4 ASJ AF: 0.00947

Gnomad4 EAS AF: 0.000560

Gnomad4 SAS AF: 0.00531

Gnomad4 FIN AF: 0.00101

Gnomad4 NFE AF: 0.00705

Gnomad4 OTH AF: 0.144

Alfa AF: 0.0922 Hom.: 992

Bravo AF: 0.218

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.78
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs725886; hg19: chrX-110745161;