rs130065
Positions:
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001105564.2(CCHCR1):c.574C>T(p.Arg192Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.202 in 1,608,406 control chromosomes in the GnomAD database, including 36,090 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.16 ( 2208 hom., cov: 32)
Exomes 𝑓: 0.21 ( 33882 hom. )
Consequence
CCHCR1
NM_001105564.2 missense
NM_001105564.2 missense
Scores
3
12
Clinical Significance
Conservation
PhyloP100: 1.50
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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.002022177).
BP6
?
Variant 6-31154723-G-A is Benign according to our data. Variant chr6-31154723-G-A is described in ClinVar as [Benign]. Clinvar id is 1242555.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.212 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCHCR1 | NM_001105564.2 | c.574C>T | p.Arg192Trp | missense_variant | 4/18 | ENST00000396268.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCHCR1 | ENST00000396268.8 | c.574C>T | p.Arg192Trp | missense_variant | 4/18 | 1 | NM_001105564.2 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.162 AC: 24639AN: 152072Hom.: 2205 Cov.: 32
GnomAD3 genomes
?
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24639
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32
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GnomAD3 exomes AF: 0.149 AC: 35749AN: 240280Hom.: 3273 AF XY: 0.152 AC XY: 20046AN XY: 131550
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GnomAD4 exome AF: 0.206 AC: 299897AN: 1456216Hom.: 33882 Cov.: 40 AF XY: 0.203 AC XY: 147349AN XY: 724744
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GnomAD4 genome ? AF: 0.162 AC: 24646AN: 152190Hom.: 2208 Cov.: 32 AF XY: 0.156 AC XY: 11600AN XY: 74402
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885
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923
ESP6500AA
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410
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1110
ExAC
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17518
Asia WGS
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247
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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 | GeneDx | Feb 17, 2020 | This variant is associated with the following publications: (PMID: 22182809) - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
D
MetaRNN
Benign
T;T;T;T;T;T;T;T;T;T;T;T;T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
P;P;P;P;P
PrimateAI
Benign
T
PROVEAN
Uncertain
D;D;D;D;D;D;D;D;D;D;D;D;D;D;D
REVEL
Benign
Sift
Benign
D;D;D;D;T;T;T;T;T;T;T;T;T;T;T
Sift4G
Uncertain
D;D;D;D;.;.;.;.;.;T;.;.;.;.;.
Polyphen
B;B;.;.;.;.;.;.;.;.;.;.;.;.;.
Vest4
MPC
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
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