Genetic Variant NM_001105564.2:c.574C>T (chr6-31154723-G-A) – ACMG Classification: Benign (-14 pts)

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

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.50

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=0.002022177).

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 rank	MANE	Protein	UniProt
CCHCR1	NM_001105564.2 link	c.574C>T	p.Arg192Trp	missense_variant	Exon 4 of 18	ENST00000396268.8	NP_001099034.1	Q8TD31-2Q769H0Q2TB68

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCHCR1	ENST00000396268.8 link	c.574C>T	p.Arg192Trp	missense_variant	Exon 4 of 18	1	NM_001105564.2	ENSP00000379566.3		Q8TD31-2

Frequencies

GnomAD3 genomes

AF:

0.162

AC:

24639

AN:

152072

Hom.:

2205

Cov.:

show subpopulations

Gnomad AFR

AF:

0.123

Gnomad AMI

AF:

0.341

Gnomad AMR

AF:

0.0968

Gnomad ASJ

AF:

0.167

Gnomad EAS

AF:

0.0398

Gnomad SAS

AF:

0.109

Gnomad FIN

AF:

0.136

Gnomad MID

AF:

0.206

Gnomad NFE

AF:

0.215

Gnomad OTH

AF:

0.145

GnomAD3 exomes

AF:

0.149

AC:

35749

AN:

240280

Hom.:

3273

AF XY:

0.152

AC XY:

20046

AN XY:

131550

show subpopulations

Gnomad AFR exome

AF:

0.125

Gnomad AMR exome

AF:

0.0693

Gnomad ASJ exome

AF:

0.175

Gnomad EAS exome

AF:

0.0313

Gnomad SAS exome

AF:

0.122

Gnomad FIN exome

AF:

0.132

Gnomad NFE exome

AF:

0.204

Gnomad OTH exome

AF:

0.160

GnomAD4 exome

AF:

0.206

AC:

299897

AN:

1456216

Hom.:

33882

Cov.:

AF XY:

0.203

AC XY:

147349

AN XY:

724744

show subpopulations

Gnomad4 AFR exome

AF:

0.115

Gnomad4 AMR exome

AF:

0.0729

Gnomad4 ASJ exome

AF:

0.183

Gnomad4 EAS exome

AF:

0.0218

Gnomad4 SAS exome

AF:

0.121

Gnomad4 FIN exome

AF:

0.136

Gnomad4 NFE exome

AF:

0.231

Gnomad4 OTH exome

AF:

0.197

GnomAD4 genome

AF:

0.162

AC:

24646

AN:

152190

Hom.:

2208

Cov.:

AF XY:

0.156

AC XY:

11600

AN XY:

74402

show subpopulations

Gnomad4 AFR

AF:

0.123

Gnomad4 AMR

AF:

0.0964

Gnomad4 ASJ

AF:

0.167

Gnomad4 EAS

AF:

0.0399

Gnomad4 SAS

AF:

0.108

Gnomad4 FIN

AF:

0.136

Gnomad4 NFE

AF:

0.215

Gnomad4 OTH

AF:

0.143

Alfa

AF:

0.200

Hom.:

6080

Bravo

AF:

0.158

TwinsUK

AF:

0.239

AC:

885

ALSPAC

AF:

0.239

AC:

923

ESP6500AA

AF:

0.136

AC:

410

ESP6500EA

AF:

0.205

AC:

1110

ExAC

AF:

0.149

AC:

17518

Asia WGS

AF:

0.0700

AC:

247

AN:

3478

EpiCase

AF:

0.212

EpiControl

AF:

0.200

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Feb 17, 2020

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is associated with the following publications: (PMID: 22182809) -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.10

BayesDel_addAF

Benign

-0.57

BayesDel_noAF

Benign

-0.45

CADD

Uncertain

DANN

Uncertain

1.0

DEOGEN2

Benign

0.021

.;T;T;.;T;T;T;.;T;T;T;.;T;.;.

Eigen

Benign

0.023

Eigen_PC

Benign

0.14

FATHMM_MKL

Benign

0.64

LIST_S2

Benign

0.84

.;.;.;T;T;T;.;T;T;T;.;T;.;.;T

MetaRNN

Benign

0.0020

T;T;T;T;T;T;T;T;T;T;T;T;T;T;T

MetaSVM

Benign

-1.1

MutationAssessor

Uncertain

2.1

.;M;.;.;.;.;.;.;.;.;.;.;.;.;.

PrimateAI

Benign

0.36

PROVEAN

Uncertain

-4.2

D;D;D;D;D;D;D;D;D;D;D;D;D;D;D

REVEL

Benign

0.080

Sift

Benign

0.039

D;D;D;D;T;T;T;T;T;T;T;T;T;T;T

Sift4G

Uncertain

0.037

D;D;D;D;.;.;.;.;.;T;.;.;.;.;.

Polyphen

0.066

B;B;.;.;.;.;.;.;.;.;.;.;.;.;.

Vest4

0.36

MPC

0.51

ClinPred

0.050

GERP RS

4.4

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Varity_R

0.094

gMVP

0.35

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