chr7-30687161-A-T

Position:

• chr7-30687161-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001202475.1(CRHR2):​c.184+2030T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.395 in 151,872 control chromosomes in the GnomAD database, including 15,922 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 0.39 (15922 hom., cov: 32)
• Consequence: CRHR2 NM_001202475.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.411

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.761 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CRHR2	NM_001202475.1	c.184+2030T>A		intron_variant			NP_001189404.1
CRHR2	NM_001202481.1	c.-166-546T>A		intron_variant			NP_001189410.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CRHR2	ENST00000348438.8	c.184+2030T>A		intron_variant		1		ENSP00000340943.4
CRHR2	ENST00000445981.5	c.184+2030T>A		intron_variant		1		ENSP00000401241.1
CRHR2	ENST00000423776.1	n.185-546T>A		intron_variant		1		ENSP00000416620.1

Frequencies

GnomAD3 genomes AF: 0.394 AC: 59843 AN: 151754 Hom.: 15877 Cov.: 32

Gnomad AFR AF: 0.767

Gnomad AMI AF: 0.346

Gnomad AMR AF: 0.328

Gnomad ASJ AF: 0.222

Gnomad EAS AF: 0.173

Gnomad SAS AF: 0.281

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.245

Gnomad OTH AF: 0.362

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

GnomAD4 genome AF: 0.395 AC: 59958 AN: 151872 Hom.: 15922 Cov.: 32 AF XY: 0.390 AC XY: 28931 AN XY: 74246

Gnomad4 AFR AF: 0.768

Gnomad4 AMR AF: 0.329

Gnomad4 ASJ AF: 0.222

Gnomad4 EAS AF: 0.173

Gnomad4 SAS AF: 0.280

Gnomad4 FIN AF: 0.225

Gnomad4 NFE AF: 0.245

Gnomad4 OTH AF: 0.363

Alfa AF: 0.311 Hom.: 1168

Bravo AF: 0.421

Asia WGS AF: 0.312 AC: 1088 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.0
DANN	Benign	0.75

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs7793837; hg19: chr7-30726777;