rs17196989
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_001105564.2(CCHCR1):c.1581-118T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0125 in 635,876 control chromosomes in the GnomAD database, including 89 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 0.010 ( 11 hom., cov: 32)
Exomes 𝑓: 0.013 ( 78 hom. )
Consequence
CCHCR1
NM_001105564.2 intron
NM_001105564.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.131
Genes affected
CCHCR1 (HGNC:13930): (coiled-coil alpha-helical rod protein 1) This gene encodes a protein with five coiled-coil alpha-helical rod domains that is thought to act as a regulator of mRNA metabolism through its interaction with mRNA-decapping protein 4. It localizes to P-bodies, the site of mRNA metabolism, with an N-terminus that is required for this subcellular localization, suggesting it is a P-body component. Naturally occurring mutations in this gene are associated with psoriasis. [provided by RefSeq, May 2017]
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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=-0.84).
BS1
?
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0101 (1537/152354) while in subpopulation SAS AF= 0.0194 (94/4834). AF 95% confidence interval is 0.0163. There are 11 homozygotes in gnomad4. There are 788 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 12 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCHCR1 | NM_001105564.2 | c.1581-118T>C | intron_variant | ENST00000396268.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCHCR1 | ENST00000396268.8 | c.1581-118T>C | intron_variant | 1 | NM_001105564.2 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0101 AC: 1538AN: 152236Hom.: 12 Cov.: 32
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GnomAD4 exome AF: 0.0133 AC: 6414AN: 483522Hom.: 78 AF XY: 0.0140 AC XY: 3563AN XY: 254850
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GnomAD4 genome ? AF: 0.0101 AC: 1537AN: 152354Hom.: 11 Cov.: 32 AF XY: 0.0106 AC XY: 788AN XY: 74504
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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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