rs11798405

chrX-5012760-A-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;