rs2267712

Variant names:

• chr7-30672618-A-C
• rs2267712
• NM_001883.5:c.230-5305T>G

Your query was ambiguous. Multiple possible variants found:

• chr7-30672618-A-C
• chr7-30672618-A-G
• chr7-30672618-A-T

Variant summary

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

The NM_001883.5(CRHR2):​c.230-5305T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.834 in 152,186 control chromosomes in the GnomAD database, including 53,107 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 0.83 (53107 hom., cov: 33)
• Consequence: CRHR2 NM_001883.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.848 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CRHR2	NM_001883.5	c.230-5305T>G		intron_variant	Intron 2 of 11	ENST00000471646.6	NP_001874.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CRHR2	ENST00000471646.6	c.230-5305T>G		intron_variant	Intron 2 of 11	1	NM_001883.5	ENSP00000418722.1

Frequencies

GnomAD3 genomes AF: 0.834 AC: 126813 AN: 152066 Hom.: 53056 Cov.: 33

Gnomad AFR AF: 0.839

Gnomad AMI AF: 0.863

Gnomad AMR AF: 0.840

Gnomad ASJ AF: 0.884

Gnomad EAS AF: 0.620

Gnomad SAS AF: 0.731

Gnomad FIN AF: 0.802

Gnomad MID AF: 0.858

Gnomad NFE AF: 0.854

Gnomad OTH AF: 0.851

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

GnomAD4 genome AF: 0.834 AC: 126920 AN: 152186 Hom.: 53107 Cov.: 33 AF XY: 0.828 AC XY: 61608 AN XY: 74410

Gnomad4 AFR AF: 0.839

Gnomad4 AMR AF: 0.840

Gnomad4 ASJ AF: 0.884

Gnomad4 EAS AF: 0.620

Gnomad4 SAS AF: 0.731

Gnomad4 FIN AF: 0.802

Gnomad4 NFE AF: 0.854

Gnomad4 OTH AF: 0.849

Alfa AF: 0.843 Hom.: 8525

Bravo AF: 0.839

Asia WGS AF: 0.719 AC: 2503 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.35
DANN	Benign	0.52

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

Other links and lift over

dbSNP: rs2267712; hg19: chr7-30712234;