rs11798405

Variant names:

• chrX-5012760-A-G
• rs11798405

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 0.0771 in 111,477 control chromosomes in the GnomAD database, including 281 homozygotes. There are 2,484 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 0.077 (281 hom., 2484 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.540

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0939 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: 0.0771 AC: 8591 AN: 111428 Hom.: 281 Cov.: 23 AF XY: 0.0738 AC XY: 2480 AN XY: 33610

Gnomad AFR AF: 0.0484

Gnomad AMI AF: 0.0878

Gnomad AMR AF: 0.0655

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.00308

Gnomad SAS AF: 0.0705

Gnomad FIN AF: 0.0793

Gnomad MID AF: 0.109

Gnomad NFE AF: 0.0961

Gnomad OTH AF: 0.0969

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

GnomAD4 genome AF: 0.0771 AC: 8591 AN: 111477 Hom.: 281 Cov.: 23 AF XY: 0.0738 AC XY: 2484 AN XY: 33669

Gnomad4 AFR AF: 0.0484

Gnomad4 AMR AF: 0.0654

Gnomad4 ASJ AF: 0.160

Gnomad4 EAS AF: 0.00309

Gnomad4 SAS AF: 0.0703

Gnomad4 FIN AF: 0.0793

Gnomad4 NFE AF: 0.0961

Gnomad4 OTH AF: 0.0964

Alfa AF: 0.0946 Hom.: 4598

Bravo AF: 0.0762

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.98
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11798405; hg19: chrX-4930801;