rs16940665
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_004382.5(CRHR1):āc.669T>Cā(p.Thr223=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.189 in 1,612,992 control chromosomes in the GnomAD database, including 32,770 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: š 0.14 ( 2139 hom., cov: 33)
Exomes š: 0.19 ( 30631 hom. )
Consequence
CRHR1
NM_004382.5 synonymous
NM_004382.5 synonymous
Scores
5
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -5.10
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_addAF=-0.802652).
BP7
?
Synonymous conserved (PhyloP=-5.1 with no splicing effect.
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 | UniProt |
---|---|---|---|---|---|---|---|
CRHR1 | NM_004382.5 | c.669T>C | p.Thr223= | synonymous_variant | 7/13 | ENST00000314537.10 | |
LINC02210-CRHR1 | NM_001256299.3 | c.144T>C | p.Thr48= | synonymous_variant | 9/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CRHR1 | ENST00000314537.10 | c.669T>C | p.Thr223= | synonymous_variant | 7/13 | 1 | NM_004382.5 | P1 | |
MAPT-AS1 | ENST00000634876.2 | n.604-1169A>G | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.144 AC: 21838AN: 152150Hom.: 2141 Cov.: 33
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GnomAD3 exomes AF: 0.145 AC: 36154AN: 248984Hom.: 3513 AF XY: 0.149 AC XY: 20025AN XY: 134848
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GnomAD4 exome AF: 0.193 AC: 282562AN: 1460724Hom.: 30631 Cov.: 34 AF XY: 0.191 AC XY: 138799AN XY: 726634
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GnomAD4 genome ? AF: 0.143 AC: 21828AN: 152268Hom.: 2139 Cov.: 33 AF XY: 0.134 AC XY: 9994AN XY: 74458
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930
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17510
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
FATHMM_MKL
Benign
N
MutationTaster
Benign
P;P;P;P;P;P
Vest4
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Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at