rs4646188

chrX-15583220-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001371415.1(ACE2):c.901-1830T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0898 in 111,503 control chromosomes in the GnomAD database, including 472 homozygotes. There are 2,927 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 0.090 (472 hom., 2927 hem., cov: 22)
• Consequence: ACE2 NM_001371415.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.915

Genes affected

ACE2 (HGNC:13557): (angiotensin converting enzyme 2) The protein encoded by this gene belongs to the angiotensin-converting enzyme family of dipeptidyl carboxydipeptidases and has considerable homology to human angiotensin 1 converting enzyme. This secreted protein catalyzes the cleavage of angiotensin I into angiotensin 1-9, and angiotensin II into the vasodilator angiotensin 1-7. ACE2 is known to be expressed in various human organs, and its organ- and cell-specific expression suggests that it may play a role in the regulation of cardiovascular and renal function, as well as fertility. In addition, the encoded protein is a functional receptor for the spike glycoprotein of the human coronavirus HCoV-NL63 and the human severe acute respiratory syndrome coronaviruses, SARS-CoV and SARS-CoV-2, the latter is the causative agent of coronavirus disease-2019 (COVID-19). Multiple splice variants have been found for this gene and the dACE2 (or MIRb-ACE2) splice variant has been found to be interferon inducible. [provided by RefSeq, Nov 2020]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.136 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ACE2	NM_001371415.1	c.901-1830T>C		intron_variant		ENST00000252519.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ACE2	ENST00000252519.8	c.901-1830T>C		intron_variant		1	NM_001371415.1	P1

Frequencies

GnomAD3 genomes AF: 0.0899 AC: 10016 AN: 111451 Hom.: 473 Cov.: 22 AF XY: 0.0872 AC XY: 2931 AN XY: 33623

Gnomad AFR AF: 0.0157

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.0436

Gnomad ASJ AF: 0.0822

Gnomad EAS AF: 0.000277

Gnomad SAS AF: 0.0790

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.0546

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.0667

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

GnomAD4 genome AF: 0.0898 AC: 10009 AN: 111503 Hom.: 472 Cov.: 22 AF XY: 0.0869 AC XY: 2927 AN XY: 33685

Gnomad4 AFR AF: 0.0157

Gnomad4 AMR AF: 0.0436

Gnomad4 ASJ AF: 0.0822

Gnomad4 EAS AF: 0.000278

Gnomad4 SAS AF: 0.0774

Gnomad4 FIN AF: 0.178

Gnomad4 NFE AF: 0.139

Gnomad4 OTH AF: 0.0659

Alfa AF: 0.114 Hom.: 714

Bravo AF: 0.0758

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	3.1
Dann	Benign	0.85

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs4646188; hg19: chrX-15601343;