6-31148433-G-C

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001105564.2(CCHCR1):​c.1552C>G​(p.Leu518Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)

Consequence

CCHCR1
NM_001105564.2 missense

Scores

1
18

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.233
Variant links:
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 Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CCHCR1NM_001105564.2 linkc.1552C>G p.Leu518Val missense_variant Exon 10 of 18 ENST00000396268.8 NP_001099034.1 Q8TD31-2Q769H0Q2TB68

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CCHCR1ENST00000396268.8 linkc.1552C>G p.Leu518Val missense_variant Exon 10 of 18 1 NM_001105564.2 ENSP00000379566.3 Q8TD31-2

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
31
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.12
BayesDel_addAF
Benign
-0.23
T
BayesDel_noAF
Benign
-0.57
CADD
Benign
22
DANN
Uncertain
1.0
DEOGEN2
Benign
0.0058
.;T;T;.
Eigen
Benign
-0.24
Eigen_PC
Benign
-0.18
FATHMM_MKL
Benign
0.64
D
LIST_S2
Benign
0.80
.;.;.;T
M_CAP
Benign
0.0055
T
MetaRNN
Benign
0.17
T;T;T;T
MetaSVM
Benign
-0.95
T
MutationAssessor
Benign
1.8
.;L;.;.
PrimateAI
Benign
0.40
T
PROVEAN
Benign
-0.87
N;N;N;N
REVEL
Benign
0.090
Sift
Benign
0.34
T;T;T;T
Sift4G
Benign
0.85
T;T;T;T
Polyphen
0.21
B;D;.;.
Vest4
0.25
MutPred
0.75
.;Gain of MoRF binding (P = 0.0835);Gain of MoRF binding (P = 0.0835);.;
MVP
0.43
MPC
0.48
ClinPred
0.10
T
GERP RS
3.3
Varity_R
0.038
gMVP
0.16

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.99
Details are displayed if max score is > 0.2
DS_DG_spliceai
0.99
Position offset: 1
DS_DL_spliceai
0.93
Position offset: -28

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr6-31116210; API