rs223686

Variant names:

• chrX-89503121-G-T
• rs223686

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 0.289 in 109,599 control chromosomes in the GnomAD database, including 3,975 homozygotes. There are 9,100 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 0.29 (3975 hom., 9100 hem., cov: 21)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.386 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: 0.289 AC: 31645 AN: 109546 Hom.: 3977 Cov.: 21 AF XY: 0.286 AC XY: 9102 AN XY: 31854

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.373

Gnomad AMR AF: 0.306

Gnomad ASJ AF: 0.375

Gnomad EAS AF: 0.0826

Gnomad SAS AF: 0.318

Gnomad FIN AF: 0.349

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.390

Gnomad OTH AF: 0.313

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

GnomAD4 genome AF: 0.289 AC: 31638 AN: 109599 Hom.: 3975 Cov.: 21 AF XY: 0.285 AC XY: 9100 AN XY: 31917

Gnomad4 AFR AF: 0.104

Gnomad4 AMR AF: 0.307

Gnomad4 ASJ AF: 0.375

Gnomad4 EAS AF: 0.0826

Gnomad4 SAS AF: 0.315

Gnomad4 FIN AF: 0.349

Gnomad4 NFE AF: 0.390

Gnomad4 OTH AF: 0.310

Alfa AF: 0.337 Hom.: 2268

Bravo AF: 0.280

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.4
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs223686; hg19: chrX-88758120;