rs3788853

chrX-129736814-C-AchrX-129736814-C-T

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 0.218 in 111,978 control chromosomes in the GnomAD database, including 1,975 homozygotes. There are 7,242 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as risk factor (no stars).

• Frequency: Genomes: 𝑓 0.22 (1975 hom., 7242 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: risk factor no assertion criteria provided O:1
• Conservation: PhyloP100: -0.577

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.234 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: 0.218 AC: 24390 AN: 111923 Hom.: 1973 Cov.: 23 AF XY: 0.212 AC XY: 7228 AN XY: 34135

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.388

Gnomad AMR AF: 0.208

Gnomad ASJ AF: 0.187

Gnomad EAS AF: 0.241

Gnomad SAS AF: 0.203

Gnomad FIN AF: 0.204

Gnomad MID AF: 0.208

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.212

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

GnomAD4 genome AF: 0.218 AC: 24404 AN: 111978 Hom.: 1975 Cov.: 23 AF XY: 0.212 AC XY: 7242 AN XY: 34200

Gnomad4 AFR AF: 0.238

Gnomad4 AMR AF: 0.208

Gnomad4 ASJ AF: 0.187

Gnomad4 EAS AF: 0.241

Gnomad4 SAS AF: 0.202

Gnomad4 FIN AF: 0.204

Gnomad4 NFE AF: 0.209

Gnomad4 OTH AF: 0.218

Alfa AF: 0.210 Hom.: 7981

Bravo AF: 0.218

ClinVar

Significance: risk factor

Submissions summary: Other:1

Revision: no assertion criteria provided

Submissions by phenotype

Susceptibility to angioedema induced by ACE inhibitors Other:1

risk factor, no assertion criteria provided

literature only

OMIM

Nov 01, 2011

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	0.0080
Dann	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3788853; hg19: chrX-128870791;