rs3795182

Variant names:

• chrX-114582351-A-G
• rs3795182

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 0.127 in 111,777 control chromosomes in the GnomAD database, including 762 homozygotes. There are 4,366 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 0.13 (762 hom., 4366 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0230
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.25 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.127 AC: 14191 AN: 111723 Hom.: 763 Cov.: 23

Gnomad AFR AF: 0.0295

Gnomad AMI AF: 0.0294

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.146

Gnomad EAS AF: 0.130

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.127 AC: 14196 AN: 111777 Hom.: 762 Cov.: 23 AF XY: 0.128 AC XY: 4366 AN XY: 33999

African (AFR) AF: 0.0295 AC: 913 AN: 30897

American (AMR) AF: 0.144 AC: 1530 AN: 10597

Ashkenazi Jewish (ASJ) AF: 0.146 AC: 386 AN: 2652

East Asian (EAS) AF: 0.131 AC: 456 AN: 3490

South Asian (SAS) AF: 0.266 AC: 703 AN: 2642

European-Finnish (FIN) AF: 0.150 AC: 902 AN: 6024

Middle Eastern (MID) AF: 0.112 AC: 24 AN: 215

European-Non Finnish (NFE) AF: 0.171 AC: 9073 AN: 53059

Other (OTH) AF: 0.124 AC: 189 AN: 1520

Alfa AF: 0.139 Hom.: 1893

Bravo AF: 0.119

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	5.8
DANN	Benign	0.59
PhyloP100		0.023

Splicing

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

Other links and lift over

dbSNP: rs3795182; hg19: chrX-113816818;