rs1912151
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_004382.5(CRHR1):c.328-3637C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.144 in 154,632 control chromosomes in the GnomAD database, including 2,190 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 0.14 ( 2142 hom., cov: 33)
Exomes 𝑓: 0.19 ( 48 hom. )
Consequence
CRHR1
NM_004382.5 intron
NM_004382.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.283
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]
LINC02210-CRHR1 (HGNC:51483): (LINC02210-CRHR1 readthrough) This locus represents naturally occurring readthrough transcription between neighboring genes CRHR1-IT1, CRHR1 intronic transcript 1 (Gene ID: 147081) and CRHR1, corticotropin releasing hormone receptor 1 (Gene ID: 1394) on chromosome 17. The readthrough transcript encodes a protein that shares sequence identity with the product of the CRHR1 gene. [provided by RefSeq, Dec 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.214 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CRHR1 | NM_004382.5 | c.328-3637C>T | intron_variant | ENST00000314537.10 | NP_004373.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CRHR1 | ENST00000314537.10 | c.328-3637C>T | intron_variant | 1 | NM_004382.5 | ENSP00000326060.6 | ||||
LINC02210-CRHR1 | ENST00000634540.1 | c.-198-3637C>T | intron_variant | 2 | ENSP00000488912.1 |
Frequencies
GnomAD3 genomes AF: 0.144 AC: 21855AN: 152200Hom.: 2144 Cov.: 33
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GnomAD3 exomes AF: 0.252 AC: 113AN: 448Hom.: 15 AF XY: 0.226 AC XY: 53AN XY: 234
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GnomAD4 exome AF: 0.191 AC: 443AN: 2314Hom.: 48 Cov.: 0 AF XY: 0.204 AC XY: 243AN XY: 1194
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GnomAD4 genome AF: 0.143 AC: 21845AN: 152318Hom.: 2142 Cov.: 33 AF XY: 0.134 AC XY: 10002AN XY: 74484
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at