rs11798405

Variant names:

• chrX-5012760-A-G
• rs11798405

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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

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

African (AFR) AF: 0.0484 AC: 1491 AN: 30784

American (AMR) AF: 0.0654 AC: 683 AN: 10437

Ashkenazi Jewish (ASJ) AF: 0.160 AC: 422 AN: 2642

East Asian (EAS) AF: 0.00309 AC: 11 AN: 3560

South Asian (SAS) AF: 0.0703 AC: 188 AN: 2673

European-Finnish (FIN) AF: 0.0793 AC: 473 AN: 5965

Middle Eastern (MID) AF: 0.106 AC: 23 AN: 216

European-Non Finnish (NFE) AF: 0.0961 AC: 5094 AN: 53002

Other (OTH) AF: 0.0964 AC: 146 AN: 1515

Alfa AF: 0.0920 Hom.: 5813

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
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs11798405; hg19: chrX-4930801;