Variant rs1800689 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_001367711.1(HRH2):c.543G>A(p.Val181Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0612 in 1,614,128 control chromosomes in the GnomAD database, including 3,333 homozygotes. 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 0.046 ( 238 hom., cov: 32)

Exomes 𝑓: 0.063 ( 3095 hom. )

Consequence

HRH2
NM_001367711.1 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.03

Variant links:

Genes affected

HRH2 (HGNC:5183): (histamine receptor H2) Histamine is a ubiquitous messenger molecule released from mast cells, enterochromaffin-like cells, and neurons. Its various actions are mediated by histamine receptors H1, H2, H3 and H4. Histamine receptor H2 belongs to the family 1 of G protein-coupled receptors. It is an integral membrane protein and stimulates gastric acid secretion. It also regulates gastrointestinal motility and intestinal secretion and is thought to be involved in regulating cell growth and differentiation. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2008]

HRH2 links:

HRH2 (HGNC:):

HRH2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.79).

BP7

Synonymous conserved (PhyloP=-1.03 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0677 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HRH2	NM_001367711.1 linkuse as main transcript	c.543G>A	p.Val181Val	synonymous_variant	2/3	ENST00000636584.2	NP_001354640.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
HRH2	ENST00000636584.2 linkuse as main transcript	c.543G>A	p.Val181Val	synonymous_variant	2/3	3	NM_001367711.1	ENSP00000489742.1	A0A1B0GTK7
HRH2	ENST00000377291.2 linkuse as main transcript	c.543G>A	p.Val181Val	synonymous_variant	2/3	1		ENSP00000366506.2	P25021-2
HRH2	ENST00000624694.2 linkuse as main transcript	n.543G>A		non_coding_transcript_exon_variant	1/3	5		ENSP00000490705.1	A0A1B0GVZ0

Frequencies

GnomAD3 genomes

AF:

0.0463

AC:

7050

AN:

152122

Hom.:

237

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0110

Gnomad AMI

AF:

0.0625

Gnomad AMR

AF:

0.0554

Gnomad ASJ

AF:

0.0746

Gnomad EAS

AF:

0.0510

Gnomad SAS

AF:

0.0738

Gnomad FIN

AF:

0.0314

Gnomad MID

AF:

0.0886

Gnomad NFE

AF:

0.0639

Gnomad OTH

AF:

0.0489

GnomAD3 exomes

AF:

0.0535

AC:

13462

AN:

251442

Hom.:

435

AF XY:

0.0555

AC XY:

7536

AN XY:

135898

show subpopulations

Gnomad AFR exome

AF:

0.0105

Gnomad AMR exome

AF:

0.0352

Gnomad ASJ exome

AF:

0.0747

Gnomad EAS exome

AF:

0.0517

Gnomad SAS exome

AF:

0.0726

Gnomad FIN exome

AF:

0.0329

Gnomad NFE exome

AF:

0.0617

Gnomad OTH exome

AF:

0.0693

GnomAD4 exome

AF:

0.0627

AC:

91697

AN:

1461886

Hom.:

3095

Cov.:

AF XY:

0.0638

AC XY:

46365

AN XY:

727240

show subpopulations

Gnomad4 AFR exome

AF:

0.00944

Gnomad4 AMR exome

AF:

0.0378

Gnomad4 ASJ exome

AF:

0.0732

Gnomad4 EAS exome

AF:

0.0436

Gnomad4 SAS exome

AF:

0.0745

Gnomad4 FIN exome

AF:

0.0328

Gnomad4 NFE exome

AF:

0.0662

Gnomad4 OTH exome

AF:

0.0636

GnomAD4 genome

AF:

0.0463

AC:

7048

AN:

152242

Hom.:

238

Cov.:

AF XY:

0.0457

AC XY:

3399

AN XY:

74432

show subpopulations

Gnomad4 AFR

AF:

0.0110

Gnomad4 AMR

AF:

0.0553

Gnomad4 ASJ

AF:

0.0746

Gnomad4 EAS

AF:

0.0509

Gnomad4 SAS

AF:

0.0740

Gnomad4 FIN

AF:

0.0314

Gnomad4 NFE

AF:

0.0640

Gnomad4 OTH

AF:

0.0475

Alfa

AF:

0.0619

Hom.:

438

Bravo

AF:

0.0454

Asia WGS

AF:

0.0530

AC:

183

AN:

3478

EpiCase

AF:

0.0667

EpiControl

AF:

0.0672

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

2.5

DANN

Benign

0.65

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over