chrX-129736814-C-A

Variant names:

• chrX-129736814-C-A
• rs3788853

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

Nov 01, 2011

OMIM

Significance: risk factor

Review Status: no assertion criteria provided

Collection Method: literature only

- -

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;