Variant rs130079 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001105564.2(CCHCR1):c.1990G>T(p.Gly664Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.224 in 1,610,436 control chromosomes in the GnomAD database, including 43,548 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.20 ( 3111 hom., cov: 31)

Exomes 𝑓: 0.23 ( 40437 hom. )

Consequence

CCHCR1
NM_001105564.2 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.76

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]

CCHCR1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0022124648).

BP6

Variant 6-31144960-C-A is Benign according to our data. Variant chr6-31144960-C-A is described in ClinVar as [Benign]. Clinvar id is 1291637.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.233 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCHCR1	NM_001105564.2 linkuse as main transcript	c.1990G>T	p.Gly664Cys	missense_variant	14/18	ENST00000396268.8	NP_001099034.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCHCR1	ENST00000396268.8 linkuse as main transcript	c.1990G>T	p.Gly664Cys	missense_variant	14/18	1	NM_001105564.2	ENSP00000379566	A2	Q8TD31-2

Frequencies

GnomAD3 genomes

AF:

0.196

AC:

29820

AN:

151982

Hom.:

3108

Cov.:

show subpopulations

Gnomad AFR

AF:

0.180

Gnomad AMI

AF:

0.346

Gnomad AMR

AF:

0.148

Gnomad ASJ

AF:

0.284

Gnomad EAS

AF:

0.0409

Gnomad SAS

AF:

0.126

Gnomad FIN

AF:

0.137

Gnomad MID

AF:

0.256

Gnomad NFE

AF:

0.236

Gnomad OTH

AF:

0.194

GnomAD3 exomes

AF:

0.177

AC:

44097

AN:

248736

Hom.:

4616

AF XY:

0.179

AC XY:

24104

AN XY:

134678

show subpopulations

Gnomad AFR exome

AF:

0.182

Gnomad AMR exome

AF:

0.116

Gnomad ASJ exome

AF:

0.298

Gnomad EAS exome

AF:

0.0318

Gnomad SAS exome

AF:

0.139

Gnomad FIN exome

AF:

0.135

Gnomad NFE exome

AF:

0.225

Gnomad OTH exome

AF:

0.198

GnomAD4 exome

AF:

0.227

AC:

331057

AN:

1458336

Hom.:

40437

Cov.:

AF XY:

0.224

AC XY:

162788

AN XY:

725632

show subpopulations

Gnomad4 AFR exome

AF:

0.178

Gnomad4 AMR exome

AF:

0.120

Gnomad4 ASJ exome

AF:

0.302

Gnomad4 EAS exome

AF:

0.0222

Gnomad4 SAS exome

AF:

0.138

Gnomad4 FIN exome

AF:

0.139

Gnomad4 NFE exome

AF:

0.249

Gnomad4 OTH exome

AF:

0.230

GnomAD4 genome

AF:

0.196

AC:

29827

AN:

152100

Hom.:

3111

Cov.:

AF XY:

0.189

AC XY:

14027

AN XY:

74350

show subpopulations

Gnomad4 AFR

AF:

0.180

Gnomad4 AMR

AF:

0.148

Gnomad4 ASJ

AF:

0.284

Gnomad4 EAS

AF:

0.0410

Gnomad4 SAS

AF:

0.125

Gnomad4 FIN

AF:

0.137

Gnomad4 NFE

AF:

0.236

Gnomad4 OTH

AF:

0.191

Alfa

AF:

0.221

Hom.:

2733

Bravo

AF:

0.198

TwinsUK

AF:

0.256

AC:

948

ALSPAC

AF:

0.258

AC:

995

ESP6500AA

AF:

0.190

AC:

835

ESP6500EA

AF:

0.236

AC:

2031

ExAC

AF:

0.178

AC:

21582

Asia WGS

AF:

0.0800

AC:

279

AN:

3478

EpiCase

AF:

0.240

EpiControl

AF:

0.228

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

Jul 13, 2018

This variant is associated with the following publications: (PMID: 29379198) -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.17

BayesDel_addAF

Benign

-0.65

BayesDel_noAF

Benign

-0.56

CADD

Benign

DANN

Uncertain

0.99

DEOGEN2

Benign

0.0085

.;T;T;.

Eigen

Benign

-0.26

Eigen_PC

Benign

-0.19

FATHMM_MKL

Benign

0.74

LIST_S2

Benign

0.67

.;.;.;T

MetaRNN

Benign

0.0022

T;T;T;T

MetaSVM

Benign

-1.0

MutationAssessor

Uncertain

2.1

.;M;.;.

MutationTaster

Benign

0.87

P;P;P;P;P

PrimateAI

Benign

0.47

PROVEAN

Benign

-2.2

N;N;N;N

REVEL

Benign

0.040

Sift

Benign

0.14

T;T;T;T

Sift4G

Benign

0.090

T;T;T;T

Polyphen

0.099

B;B;.;.

Vest4

0.31

MPC

0.59

ClinPred

0.014

GERP RS

1.5

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Varity_R

0.13

gMVP

0.16

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over