chrX-15584941-G-C

Variant names:

• chrX-15584941-G-C
• rs4646142
• NM_001371415.1:c.900+534C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001371415.1(ACE2):​c.900+534C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 111,009 control chromosomes in the GnomAD database, including 2,612 homozygotes. There are 8,181 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 0.25 (2612 hom., 8181 hem., cov: 23)
• Consequence: ACE2 NM_001371415.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.582
• Publications: 26 publications found

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]

ENSG00000285602 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.51 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ACE2	NM_001371415.1	c.900+534C>G		intron_variant	Intron 7 of 17	ENST00000252519.8	NP_001358344.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ACE2	ENST00000252519.8	c.900+534C>G		intron_variant	Intron 7 of 17	1	NM_001371415.1	ENSP00000252519.3
ENSG00000285602	ENST00000649243.1	n.*978+534C>G		intron_variant	Intron 12 of 19			ENSP00000497489.1

Frequencies

GnomAD3 genomes AF: 0.245 AC: 27211 AN: 110957 Hom.: 2612 Cov.: 23

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.194

Gnomad AMR AF: 0.371

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.530

Gnomad SAS AF: 0.449

Gnomad FIN AF: 0.187

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.203

Gnomad OTH AF: 0.237

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

GnomAD4 genome AF: 0.245 AC: 27227 AN: 111009 Hom.: 2612 Cov.: 23 AF XY: 0.246 AC XY: 8181 AN XY: 33313

African (AFR) AF: 0.237 AC: 7239 AN: 30534

American (AMR) AF: 0.371 AC: 3883 AN: 10464

Ashkenazi Jewish (ASJ) AF: 0.261 AC: 688 AN: 2634

East Asian (EAS) AF: 0.530 AC: 1859 AN: 3510

South Asian (SAS) AF: 0.449 AC: 1172 AN: 2612

European-Finnish (FIN) AF: 0.187 AC: 1111 AN: 5927

Middle Eastern (MID) AF: 0.200 AC: 43 AN: 215

European-Non Finnish (NFE) AF: 0.203 AC: 10738 AN: 52924

Other (OTH) AF: 0.240 AC: 364 AN: 1519

Alfa AF: 0.0973 Hom.: 477

Bravo AF: 0.261

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	0.68
DANN	Benign	0.82
PhyloP100		-0.58
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs4646142; hg19: chrX-15603064;