rs3795182

chrX-114582351-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 0.127 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.127 AC: 14191 AN: 111723 Hom.: 763 Cov.: 23 AF XY: 0.128 AC XY: 4359 AN XY: 33937

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

Gnomad4 AFR AF: 0.0295

Gnomad4 AMR AF: 0.144

Gnomad4 ASJ AF: 0.146

Gnomad4 EAS AF: 0.131

Gnomad4 SAS AF: 0.266

Gnomad4 FIN AF: 0.150

Gnomad4 NFE AF: 0.171

Gnomad4 OTH AF: 0.124

Alfa AF: 0.148 Hom.: 863

Bravo AF: 0.119

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
Cadd	Benign	5.8
Dann	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3795182; hg19: chrX-113816818;