Variant chr7-30655586-C-T details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001883.5(CRHR2):c.1047G>A(p.Ser349=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0969 in 1,611,880 control chromosomes in the GnomAD database, including 8,740 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 0.099 ( 834 hom., cov: 33)

Exomes 𝑓: 0.097 ( 7906 hom. )

Consequence

CRHR2
NM_001883.5 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.94

Variant links:

Genes affected

CRHR2 (HGNC:2358): (corticotropin releasing hormone receptor 2) The protein encoded by this gene belongs to the G-protein coupled receptor 2 family, and the subfamily of corticotropin releasing hormone receptor. This receptor shows high affinity for corticotropin releasing hormone (CRH), and also binds CRH-related peptides such as urocortin. CRH is synthesized in the hypothalamus, and plays an important role in coordinating the endocrine, autonomic, and behavioral responses to stress and immune challenge. Studies in mice suggest that this receptor maybe involved in mediating cardiovascular homeostasis. Alternatively spliced transcript variants encoding different isoforms have been described for this gene.[provided by RefSeq, Jan 2011]

CRHR2 links:

LOC124901609 (HGNC:):

LOC124901609 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=-0.49).

BP7

Synonymous conserved (PhyloP=-2.94 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.187 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CRHR2	NM_001883.5 linkuse as main transcript	c.1047G>A	p.Ser349=	synonymous_variant	10/12	ENST00000471646.6	NP_001874.2
LOC124901609	XR_007060276.1 linkuse as main transcript	n.1790C>T		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CRHR2	ENST00000471646.6 linkuse as main transcript	c.1047G>A	p.Ser349=	synonymous_variant	10/12	1	NM_001883.5	ENSP00000418722	P1	Q13324-1

Frequencies

GnomAD3 genomes

AF:

0.0992

AC:

15086

AN:

152142

Hom.:

831

Cov.:

show subpopulations

Gnomad AFR

AF:

0.110

Gnomad AMI

AF:

0.0143

Gnomad AMR

AF:

0.0940

Gnomad ASJ

AF:

0.0936

Gnomad EAS

AF:

0.181

Gnomad SAS

AF:

0.197

Gnomad FIN

AF:

0.0611

Gnomad MID

AF:

0.108

Gnomad NFE

AF:

0.0868

Gnomad OTH

AF:

0.126

GnomAD3 exomes

AF:

0.107

AC:

26593

AN:

249494

Hom.:

1697

AF XY:

0.110

AC XY:

14874

AN XY:

134808

show subpopulations

Gnomad AFR exome

AF:

0.111

Gnomad AMR exome

AF:

0.0754

Gnomad ASJ exome

AF:

0.102

Gnomad EAS exome

AF:

0.162

Gnomad SAS exome

AF:

0.194

Gnomad FIN exome

AF:

0.0623

Gnomad NFE exome

AF:

0.0920

Gnomad OTH exome

AF:

0.106

GnomAD4 exome

AF:

0.0967

AC:

141162

AN:

1459618

Hom.:

7906

Cov.:

AF XY:

0.0994

AC XY:

72176

AN XY:

726016

show subpopulations

Gnomad4 AFR exome

AF:

0.110

Gnomad4 AMR exome

AF:

0.0766

Gnomad4 ASJ exome

AF:

0.100

Gnomad4 EAS exome

AF:

0.192

Gnomad4 SAS exome

AF:

0.189

Gnomad4 FIN exome

AF:

0.0622

Gnomad4 NFE exome

AF:

0.0873

Gnomad4 OTH exome

AF:

0.109

GnomAD4 genome

AF:

0.0992

AC:

15099

AN:

152262

Hom.:

834

Cov.:

AF XY:

0.100

AC XY:

7468

AN XY:

74440

show subpopulations

Gnomad4 AFR

AF:

0.110

Gnomad4 AMR

AF:

0.0938

Gnomad4 ASJ

AF:

0.0936

Gnomad4 EAS

AF:

0.181

Gnomad4 SAS

AF:

0.197

Gnomad4 FIN

AF:

0.0611

Gnomad4 NFE

AF:

0.0867

Gnomad4 OTH

AF:

0.130

Alfa

AF:

0.0796

Hom.:

323

Bravo

AF:

0.102

Asia WGS

AF:

0.214

AC:

743

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.49

CADD

Benign

0.68

DANN

Benign

0.71

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