chr5-76953678-G-A
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_001882.4(CRHBP):c.159G>A(p.Pro53=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00624 in 1,609,112 control chromosomes in the GnomAD database, including 61 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0051 ( 8 hom., cov: 33)
Exomes 𝑓: 0.0064 ( 53 hom. )
Consequence
CRHBP
NM_001882.4 synonymous
NM_001882.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0990
Genes affected
CRHBP (HGNC:2356): (corticotropin releasing hormone binding protein) Corticotropin-releasing hormone is a potent stimulator of synthesis and secretion of preopiomelanocortin-derived peptides. Although CRH concentrations in the human peripheral circulation are normally low, they increase throughout pregnancy and fall rapidly after parturition. Maternal plasma CRH probably originates from the placenta. Human plasma contains a CRH-binding protein which inactivates CRH and which may prevent inappropriate pituitary-adrenal stimulation in pregnancy. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.53).
BP6
?
Variant 5-76953678-G-A is Benign according to our data. Variant chr5-76953678-G-A is described in ClinVar as [Benign]. Clinvar id is 711390.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-0.099 with no splicing effect.
BS2
?
High Homozygotes in GnomAd at 8 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CRHBP | NM_001882.4 | c.159G>A | p.Pro53= | synonymous_variant | 2/7 | ENST00000274368.9 | |
CRHBP | XM_047416736.1 | c.-74G>A | 5_prime_UTR_variant | 1/6 | |||
CRHBP | XR_948235.4 | n.249G>A | non_coding_transcript_exon_variant | 2/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CRHBP | ENST00000274368.9 | c.159G>A | p.Pro53= | synonymous_variant | 2/7 | 1 | NM_001882.4 | P1 | |
CRHBP | ENST00000506501.1 | c.159G>A | p.Pro53= | synonymous_variant | 2/5 | 1 | |||
CRHBP | ENST00000512446.1 | n.262G>A | non_coding_transcript_exon_variant | 1/4 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00513 AC: 781AN: 152172Hom.: 8 Cov.: 33
GnomAD3 genomes
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GnomAD3 exomes AF: 0.00412 AC: 966AN: 234540Hom.: 5 AF XY: 0.00387 AC XY: 496AN XY: 128116
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GnomAD4 exome AF: 0.00635 AC: 9256AN: 1456824Hom.: 53 Cov.: 31 AF XY: 0.00617 AC XY: 4472AN XY: 724210
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GnomAD4 genome ? AF: 0.00513 AC: 781AN: 152288Hom.: 8 Cov.: 33 AF XY: 0.00465 AC XY: 346AN XY: 74458
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Aug 15, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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