rs2223713

Positions:

• chrX-86110417-A-C

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 0.278 in 111,090 control chromosomes in the GnomAD database, including 3,603 homozygotes. There are 8,751 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 0.28 (3603 hom., 8751 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.164

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 (AMR) allele frequency at 95% confidence interval = 0.367 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: 0.278 AC: 30892 AN: 111039 Hom.: 3605 Cov.: 23 AF XY: 0.263 AC XY: 8744 AN XY: 33257

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.390

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.326

Gnomad EAS AF: 0.00365

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.340

Gnomad OTH AF: 0.288

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

GnomAD4 genome AF: 0.278 AC: 30895 AN: 111090 Hom.: 3603 Cov.: 23 AF XY: 0.263 AC XY: 8751 AN XY: 33318

Gnomad4 AFR AF: 0.165

Gnomad4 AMR AF: 0.376

Gnomad4 ASJ AF: 0.326

Gnomad4 EAS AF: 0.00366

Gnomad4 SAS AF: 0.161

Gnomad4 FIN AF: 0.315

Gnomad4 NFE AF: 0.340

Gnomad4 OTH AF: 0.284

Alfa AF: 0.301 Hom.: 2722

Bravo AF: 0.284

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.4
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: rs2223713; hg19: chrX-85365421;