chrX-15583220-A-G

Variant names:

• chrX-15583220-A-G
• rs4646188
• NM_001371415.1:c.901-1830T>C

Variant summary

Our verdict is Benign. The variant received -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]

ENSG00000285602 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
ACE2	NM_001371415.1	c.901-1830T>C		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.901-1830T>C		intron_variant	Intron 7 of 17	1	NM_001371415.1	ENSP00000252519.3
ENSG00000285602	ENST00000649243.1	n.*979-1830T>C		intron_variant	Intron 12 of 19			ENSP00000497489.1

Frequencies

GnomAD3 genomes AF: 0.0899 AC: 10016 AN: 111451 Hom.: 473 Cov.: 22

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

African (AFR) AF: 0.0157 AC: 483 AN: 30827

American (AMR) AF: 0.0436 AC: 458 AN: 10510

Ashkenazi Jewish (ASJ) AF: 0.0822 AC: 216 AN: 2627

East Asian (EAS) AF: 0.000278 AC: 1 AN: 3602

South Asian (SAS) AF: 0.0774 AC: 208 AN: 2689

European-Finnish (FIN) AF: 0.178 AC: 1043 AN: 5857

Middle Eastern (MID) AF: 0.0553 AC: 12 AN: 217

European-Non Finnish (NFE) AF: 0.139 AC: 7375 AN: 53000

Other (OTH) AF: 0.0659 AC: 99 AN: 1503

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
PhyloP100		0.92
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

Publications

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Other links and lift over

dbSNP: rs4646188; hg19: chrX-15601343;