rs973002

Positions:

• chr7-30659288-G-A
• chr7-30659288-G-C

Variant summary

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

The NM_001883.5(CRHR2):​c.831+1285C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.831 in 152,212 control chromosomes in the GnomAD database, including 52,834 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 (52834 hom., cov: 32)
• Consequence: CRHR2 NM_001883.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.797

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]

LOC124901609 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.873 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CRHR2	NM_001883.5	c.831+1285C>T		intron_variant		ENST00000471646.6
LOC124901609	XR_007060276.1	n.5492G>A		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CRHR2	ENST00000471646.6	c.831+1285C>T		intron_variant		1	NM_001883.5	P1

Frequencies

GnomAD3 genomes AF: 0.831 AC: 126450 AN: 152092 Hom.: 52782 Cov.: 32

Gnomad AFR AF: 0.881

Gnomad AMI AF: 0.816

Gnomad AMR AF: 0.832

Gnomad ASJ AF: 0.842

Gnomad EAS AF: 0.645

Gnomad SAS AF: 0.697

Gnomad FIN AF: 0.793

Gnomad MID AF: 0.842

Gnomad NFE AF: 0.830

Gnomad OTH AF: 0.843

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

GnomAD4 genome AF: 0.831 AC: 126559 AN: 152212 Hom.: 52834 Cov.: 32 AF XY: 0.826 AC XY: 61476 AN XY: 74416

Gnomad4 AFR AF: 0.881

Gnomad4 AMR AF: 0.832

Gnomad4 ASJ AF: 0.842

Gnomad4 EAS AF: 0.645

Gnomad4 SAS AF: 0.698

Gnomad4 FIN AF: 0.793

Gnomad4 NFE AF: 0.830

Gnomad4 OTH AF: 0.842

Alfa AF: 0.833 Hom.: 18019

Bravo AF: 0.839

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.12
DANN	Benign	0.43

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: rs973002; hg19: chr7-30698904;