X-116172342-G-T

Position:

chrX-116172342-G-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_ModerateBP6_Very_StrongBS2

The NM_000686.5(AGTR2):c.62G>T(p.Gly21Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00403 in 1,208,856 control chromosomes in the GnomAD database, including 13 homozygotes. There are 1,581 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G21R) has been classified as Uncertain significance.

Frequency

Genomes: 𝑓 0.0027 ( 2 hom., 76 hem., cov: 23)

Exomes 𝑓: 0.0042 ( 11 hom. 1505 hem. )

Consequence

AGTR2
NM_000686.5 missense

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts U:1B:6

Conservation

PhyloP100: 0.485

Variant links:

Genes affected

AGTR2 (HGNC:338): (angiotensin II receptor type 2) The protein encoded by this gene belongs to the G-protein coupled receptor 1 family, and functions as a receptor for angiotensin II. It is an intergral membrane protein that is highly expressed in fetus and in neonates, but scantily in adult tissues, except brain, adrenal medulla, and atretic ovary. This receptor has been shown to mediate programmed cell death and this apoptotic function may play an important role in developmental biology and pathophysiology. Mutations in this gene are been associated with X-linked cognitive disability. Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) and SARS-CoV-2 infection results in down-regulation of angiotensin converting enzyme-2 (ACE2) receptors, the effects of which, triggers serious inflammatory lesions in the tissues involved, primarily in the lungs. The inflammatory reaction appears to be mediated by angiotensin II derivatives, including the angiotensin AT2 receptor which has been found to be upregulated in bronchoalveolar lavage samples from Coronavirus disease 2019 (COVID19) patients. [provided by RefSeq, Jul 2020]

AGTR2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0701001).

BP6

Variant X-116172342-G-T is Benign according to our data. Variant chrX-116172342-G-T is described in ClinVar as [Likely_benign]. Clinvar id is 11716.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-116172342-G-T is described in Lovd as [Likely_benign]. Variant chrX-116172342-G-T is described in Lovd as [Benign].

BS2

High Homozygotes in GnomAd4 at 2 XL gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AGTR2	NM_000686.5 linkuse as main transcript	c.62G>T	p.Gly21Val	missense_variant	3/3	ENST00000371906.5
AGTR2	NM_001385624.1 linkuse as main transcript	c.62G>T	p.Gly21Val	missense_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris
AGTR2	ENST00000371906.5 linkuse as main transcript	c.62G>T	p.Gly21Val	missense_variant	3/3	1	NM_000686.5	P1
AGTR2	ENST00000681852.1 linkuse as main transcript	c.62G>T	p.Gly21Val	missense_variant	2/2			P1
AGTR2	ENST00000680409.1 linkuse as main transcript	n.530G>T		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes

AF:

0.00273

AC:

304

AN:

111214

Hom.:

Cov.:

AF XY:

0.00233

AC XY:

AN XY:

33490

show subpopulations

Gnomad AFR

AF:

0.000426

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00335

Gnomad ASJ

AF:

0.00114

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00188

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00837

Gnomad NFE

AF:

0.00453

Gnomad OTH

AF:

0.00401

GnomAD3 exomes

AF:

0.00251

AC:

459

AN:

183135

Hom.:

AF XY:

0.00253

AC XY:

171

AN XY:

67693

show subpopulations

Gnomad AFR exome

AF:

0.000532

Gnomad AMR exome

AF:

0.00256

Gnomad ASJ exome

AF:

0.00147

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00152

Gnomad FIN exome

AF:

0.0000625

Gnomad NFE exome

AF:

0.00410

Gnomad OTH exome

AF:

0.00133

GnomAD4 exome

AF:

0.00417

AC:

4576

AN:

1097590

Hom.:

Cov.:

AF XY:

0.00414

AC XY:

1505

AN XY:

363134

show subpopulations

Gnomad4 AFR exome

AF:

0.000531

Gnomad4 AMR exome

AF:

0.00256

Gnomad4 ASJ exome

AF:

0.000878

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00170

Gnomad4 FIN exome

AF:

0.000123

Gnomad4 NFE exome

AF:

0.00490

Gnomad4 OTH exome

AF:

0.00417

GnomAD4 genome

AF:

0.00271

AC:

301

AN:

111266

Hom.:

Cov.:

AF XY:

0.00227

AC XY:

AN XY:

33552

show subpopulations

Gnomad4 AFR

AF:

0.000425

Gnomad4 AMR

AF:

0.00335

Gnomad4 ASJ

AF:

0.00114

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00113

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.00453

Gnomad4 OTH

AF:

0.00330

Alfa

AF:

0.00422

Hom.:

175

Bravo

AF:

0.00291

TwinsUK

AF:

0.00485

AC:

ALSPAC

AF:

0.00588

AC:

ESP6500AA

AF:

0.000522

AC:

ESP6500EA

AF:

0.00461

AC:

ExAC

AF:

0.00249

AC:

302

EpiCase

AF:

0.00551

EpiControl

AF:

0.00582

ClinVar

Significance: Benign/Likely benign

Submissions summary: Uncertain:1Benign:6

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Uncertain:1Benign:2

Uncertain significance, no assertion criteria provided	literature only	OMIM	Aug 08, 2013	- -
Likely benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Likely benign, no assertion criteria provided	clinical testing	Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)	-	- -

not specified

Benign:3

Benign, no assertion criteria provided	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	-	- -
Benign, criteria provided, single submitter	clinical testing	Genetic Services Laboratory, University of Chicago	Jul 15, 2013	- -
Likely benign, criteria provided, single submitter	clinical testing	Ambry Genetics	Dec 11, 2015	This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

Intellectual disability, X-linked 88

Benign:1

Likely benign, no assertion criteria provided

clinical testing

Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.26

BayesDel_addAF

Benign

-0.20

BayesDel_noAF

Uncertain

-0.050

CADD

Benign

1.7

DANN

Benign

0.44

DEOGEN2

Benign

0.36

FATHMM_MKL

Benign

0.093

LIST_S2

Benign

0.37

M_CAP

Benign

0.035

MetaRNN

Benign

0.070

MetaSVM

Benign

-0.89

MutationAssessor

Benign

0.34

MutationTaster

Benign

0.000013

PrimateAI

Benign

0.21

PROVEAN

Benign

-0.35

REVEL

Uncertain

0.37

Sift

Benign

0.20

Sift4G

Benign

0.22

Polyphen

0.0

Vest4

0.055

MVP

0.85

MPC

0.18

ClinPred

0.0015

GERP RS

3.6

Varity_R

0.062

gMVP

0.48

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over