rs725886

Positions:

• chrX-111501933-C-A

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;