rs223686

Positions:

• chrX-89503121-G-T

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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365

Genes affected

(HGNC:):

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/exons	MANE	Protein	UniProt
		n.89503121G>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;