ENST00000348438.8:c.184+2030T>A

Variant names:

• chr7-30687161-A-T
• rs7793837
• ENST00000348438.8:c.184+2030T>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000348438.8(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 ENST00000348438.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.411
• Publications: 18 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000348438.8. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CRHR2	NM_001202475.1		c.184+2030T>A		intron	N/A	NP_001189404.1
	CRHR2	NM_001202481.1		c.-166-546T>A		intron	N/A	NP_001189410.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CRHR2	ENST00000348438.8	TSL:1	c.184+2030T>A		intron	N/A	ENSP00000340943.4
	CRHR2	ENST00000445981.5	TSL:1	c.184+2030T>A		intron	N/A	ENSP00000401241.1
	CRHR2	ENST00000423776.1	TSL:1	n.185-546T>A		intron	N/A	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

African (AFR) AF: 0.768 AC: 31771 AN: 41384

American (AMR) AF: 0.329 AC: 5013 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.222 AC: 771 AN: 3466

East Asian (EAS) AF: 0.173 AC: 892 AN: 5152

South Asian (SAS) AF: 0.280 AC: 1347 AN: 4808

European-Finnish (FIN) AF: 0.225 AC: 2376 AN: 10574

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.245 AC: 16619 AN: 67942

Other (OTH) AF: 0.363 AC: 762 AN: 2100

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.0
DANN	Benign	0.75
PhyloP100		0.41
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs7793837; hg19: chr7-30726777;