rs2014663
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001883.5(CRHR2):c.229+5958G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.871 in 152,232 control chromosomes in the GnomAD database, including 58,242 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 0.87 ( 58242 hom., cov: 32)
Consequence
CRHR2
NM_001883.5 intron
NM_001883.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.783
Publications
8 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]
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.96).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.961 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CRHR2 | NM_001883.5 | c.229+5958G>A | intron_variant | Intron 2 of 11 | ENST00000471646.6 | NP_001874.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.871 AC: 132483AN: 152114Hom.: 58184 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
132483
AN:
152114
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.871 AC: 132600AN: 152232Hom.: 58242 Cov.: 32 AF XY: 0.864 AC XY: 64282AN XY: 74422 show subpopulations
GnomAD4 genome
AF:
AC:
132600
AN:
152232
Hom.:
Cov.:
32
AF XY:
AC XY:
64282
AN XY:
74422
show subpopulations
African (AFR)
AF:
AC:
40275
AN:
41566
American (AMR)
AF:
AC:
13094
AN:
15304
Ashkenazi Jewish (ASJ)
AF:
AC:
3068
AN:
3470
East Asian (EAS)
AF:
AC:
3176
AN:
5166
South Asian (SAS)
AF:
AC:
3521
AN:
4812
European-Finnish (FIN)
AF:
AC:
8495
AN:
10588
Middle Eastern (MID)
AF:
AC:
257
AN:
292
European-Non Finnish (NFE)
AF:
AC:
58081
AN:
68014
Other (OTH)
AF:
AC:
1849
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
Heterozygous variant carriers
0
866
1732
2599
3465
4331
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
888
1776
2664
3552
4440
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
2516
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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