rs17159371

Variant names:

• chr7-30690056-A-C
• rs17159371
• ENST00000348438.8:c.91-772T>G

Your query was ambiguous. Multiple possible variants found:

• chr7-30690056-A-C
• chr7-30690056-A-G

Variant summary

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

The ENST00000348438.8(CRHR2):​c.91-772T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0813 in 152,278 control chromosomes in the GnomAD database, including 568 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 0.081 (568 hom., cov: 33)
• Consequence: CRHR2 ENST00000348438.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.622
• Publications: 9 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.119 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CRHR2	NM_001202475.1	c.91-772T>G		intron_variant	Intron 1 of 12		NP_001189404.1
CRHR2	NM_001202481.1	c.-260-772T>G		intron_variant	Intron 1 of 13		NP_001189410.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CRHR2	ENST00000348438.8	c.91-772T>G		intron_variant	Intron 1 of 12	1		ENSP00000340943.4
CRHR2	ENST00000445981.5	c.91-772T>G		intron_variant	Intron 1 of 2	1		ENSP00000401241.1
CRHR2	ENST00000423776.1	n.91-772T>G		intron_variant	Intron 1 of 3	1		ENSP00000416620.1

Frequencies

GnomAD3 genomes AF: 0.0813 AC: 12366 AN: 152160 Hom.: 564 Cov.: 33

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.0735

Gnomad AMR AF: 0.123

Gnomad ASJ AF: 0.0380

Gnomad EAS AF: 0.00212

Gnomad SAS AF: 0.0521

Gnomad FIN AF: 0.0904

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0696

Gnomad OTH AF: 0.0684

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

GnomAD4 genome AF: 0.0813 AC: 12380 AN: 152278 Hom.: 568 Cov.: 33 AF XY: 0.0820 AC XY: 6105 AN XY: 74464

African (AFR) AF: 0.101 AC: 4180 AN: 41560

American (AMR) AF: 0.124 AC: 1896 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0380 AC: 132 AN: 3470

East Asian (EAS) AF: 0.00231 AC: 12 AN: 5186

South Asian (SAS) AF: 0.0517 AC: 249 AN: 4814

European-Finnish (FIN) AF: 0.0904 AC: 960 AN: 10620

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0696 AC: 4731 AN: 68014

Other (OTH) AF: 0.0672 AC: 142 AN: 2112

Alfa AF: 0.0674 Hom.: 322

Bravo AF: 0.0855

Asia WGS AF: 0.0340 AC: 118 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.67
DANN	Benign	0.36
PhyloP100		-0.62
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: rs17159371; hg19: chr7-30729672;