rs11798018

Variant names:

• chrX-100584573-C-A
• rs11798018

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 0.254 in 111,273 control chromosomes in the GnomAD database, including 3,389 homozygotes. There are 8,766 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 0.25 (3389 hom., 8766 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.86

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 (EAS) allele frequency at 95% confidence interval = 0.692 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: 0.255 AC: 28314 AN: 111218 Hom.: 3393 Cov.: 23 AF XY: 0.262 AC XY: 8761 AN XY: 33446

Gnomad AFR AF: 0.0509

Gnomad AMI AF: 0.379

Gnomad AMR AF: 0.358

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.715

Gnomad SAS AF: 0.393

Gnomad FIN AF: 0.384

Gnomad MID AF: 0.248

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.272

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

GnomAD4 genome AF: 0.254 AC: 28304 AN: 111273 Hom.: 3389 Cov.: 23 AF XY: 0.262 AC XY: 8766 AN XY: 33511

Gnomad4 AFR AF: 0.0508

Gnomad4 AMR AF: 0.358

Gnomad4 ASJ AF: 0.241

Gnomad4 EAS AF: 0.715

Gnomad4 SAS AF: 0.392

Gnomad4 FIN AF: 0.384

Gnomad4 NFE AF: 0.299

Gnomad4 OTH AF: 0.269

Alfa AF: 0.298 Hom.: 12739

Bravo AF: 0.251

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	1.4
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: rs11798018; hg19: chrX-99839570;