chrX-86110417-A-C

Variant names:

• chrX-86110417-A-C
• rs2223713

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 0.278 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.278 AC: 30892 AN: 111039 Hom.: 3605 Cov.: 23

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

African (AFR) AF: 0.165 AC: 5064 AN: 30666

American (AMR) AF: 0.376 AC: 3902 AN: 10364

Ashkenazi Jewish (ASJ) AF: 0.326 AC: 859 AN: 2631

East Asian (EAS) AF: 0.00366 AC: 13 AN: 3549

South Asian (SAS) AF: 0.161 AC: 430 AN: 2665

European-Finnish (FIN) AF: 0.315 AC: 1875 AN: 5952

Middle Eastern (MID) AF: 0.298 AC: 62 AN: 208

European-Non Finnish (NFE) AF: 0.340 AC: 17997 AN: 52865

Other (OTH) AF: 0.284 AC: 430 AN: 1515

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
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs2223713; hg19: chrX-85365421;