rs4792887
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_004382.5(CRHR1):c.34-7356C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.156 in 152,114 control chromosomes in the GnomAD database, including 2,856 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 0.16 ( 2856 hom., cov: 33)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
CRHR1
NM_004382.5 intron
NM_004382.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.88
Genes affected
CRHR1 (HGNC:2357): (corticotropin releasing hormone receptor 1) This gene encodes a G-protein coupled receptor that binds neuropeptides of the corticotropin releasing hormone family that are major regulators of the hypothalamic-pituitary-adrenal pathway. The encoded protein is essential for the activation of signal transduction pathways that regulate diverse physiological processes including stress, reproduction, immune response and obesity. Alternative splicing results in multiple transcript variants. Naturally-occurring readthrough transcription between this gene and upstream GeneID:147081 results in transcripts that encode isoforms that share similarity with the products of this gene. [provided by RefSeq, Aug 2016]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.332 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CRHR1 | NM_004382.5 | c.34-7356C>T | intron_variant | ENST00000314537.10 | |||
LINC02210-CRHR1 | NM_001256299.3 | c.-492-7356C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CRHR1 | ENST00000314537.10 | c.34-7356C>T | intron_variant | 1 | NM_004382.5 | P1 | |||
MAPT-AS1 | ENST00000634876.2 | n.3369G>A | non_coding_transcript_exon_variant | 7/7 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.156 AC: 23726AN: 151996Hom.: 2838 Cov.: 33
GnomAD3 genomes
?
AF:
AC:
23726
AN:
151996
Hom.:
Cov.:
33
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:
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 24Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 22
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
24
Hom.:
Cov.:
0
AF XY:
AC XY:
0
AN XY:
22
Gnomad4 AFR exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 NFE exome
AF:
GnomAD4 genome ? AF: 0.156 AC: 23800AN: 152114Hom.: 2856 Cov.: 33 AF XY: 0.153 AC XY: 11398AN XY: 74386
GnomAD4 genome
?
AF:
AC:
23800
AN:
152114
Hom.:
Cov.:
33
AF XY:
AC XY:
11398
AN XY:
74386
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
148
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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