Variant 6-31150734-T-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000396268.8(CCHCR1):c.1092A>C(p.Glu364Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.206 in 1,611,990 control chromosomes in the GnomAD database, including 35,893 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.21 ( 3489 hom., cov: 32)

Exomes 𝑓: 0.21 ( 32404 hom. )

Consequence

CCHCR1
ENST00000396268.8 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.382

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:

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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 (MetaRNN=0.005039245).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.327 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.1092A>C	p.Glu364Asp	missense_variant	6/18	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.1092A>C	p.Glu364Asp	missense_variant	6/18	1	NM_001105564.2	ENSP00000379566	A2	Q8TD31-2

Frequencies

GnomAD3 genomes

AF:

0.210

AC:

31944

AN:

152050

Hom.:

3488

Cov.:

show subpopulations

Gnomad AFR

AF:

0.195

Gnomad AMI

AF:

0.104

Gnomad AMR

AF:

0.286

Gnomad ASJ

AF:

0.107

Gnomad EAS

AF:

0.339

Gnomad SAS

AF:

0.245

Gnomad FIN

AF:

0.224

Gnomad MID

AF:

0.191

Gnomad NFE

AF:

0.195

Gnomad OTH

AF:

0.189

GnomAD3 exomes

AF:

0.229

AC:

56419

AN:

246656

Hom.:

6990

AF XY:

0.225

AC XY:

30208

AN XY:

134340

show subpopulations

Gnomad AFR exome

AF:

0.192

Gnomad AMR exome

AF:

0.313

Gnomad ASJ exome

AF:

0.0983

Gnomad EAS exome

AF:

0.335

Gnomad SAS exome

AF:

0.239

Gnomad FIN exome

AF:

0.232

Gnomad NFE exome

AF:

0.199

Gnomad OTH exome

AF:

0.217

GnomAD4 exome

AF:

0.206

AC:

300287

AN:

1459822

Hom.:

32404

Cov.:

AF XY:

0.205

AC XY:

149225

AN XY:

726240

show subpopulations

Gnomad4 AFR exome

AF:

0.190

Gnomad4 AMR exome

AF:

0.309

Gnomad4 ASJ exome

AF:

0.102

Gnomad4 EAS exome

AF:

0.339

Gnomad4 SAS exome

AF:

0.243

Gnomad4 FIN exome

AF:

0.228

Gnomad4 NFE exome

AF:

0.196

Gnomad4 OTH exome

AF:

0.194

GnomAD4 genome

AF:

0.210

AC:

31959

AN:

152168

Hom.:

3489

Cov.:

AF XY:

0.214

AC XY:

15898

AN XY:

74382

show subpopulations

Gnomad4 AFR

AF:

0.195

Gnomad4 AMR

AF:

0.286

Gnomad4 ASJ

AF:

0.107

Gnomad4 EAS

AF:

0.340

Gnomad4 SAS

AF:

0.244

Gnomad4 FIN

AF:

0.224

Gnomad4 NFE

AF:

0.195

Gnomad4 OTH

AF:

0.192

Alfa

AF:

0.194

Hom.:

6455

Bravo

AF:

0.214

TwinsUK

AF:

0.206

AC:

764

ALSPAC

AF:

0.198

AC:

763

ESP6500AA

AF:

0.192

AC:

580

ESP6500EA

AF:

0.197

AC:

1069

ExAC

AF:

0.227

AC:

26974

Asia WGS

AF:

0.312

AC:

1083

AN:

3478

EpiCase

AF:

0.178

EpiControl

AF:

0.180

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.11

BayesDel_addAF

Benign

-0.74

BayesDel_noAF

Benign

-0.69

CADD

Benign

5.8

DANN

Benign

0.97

DEOGEN2

Benign

0.0032

.;T;T;.

Eigen

Benign

-1.0

Eigen_PC

Benign

-1.0

FATHMM_MKL

Benign

0.026

LIST_S2

Benign

0.60

.;.;.;T

MetaRNN

Benign

0.0050

T;T;T;T

MetaSVM

Benign

-0.90

MutationAssessor

Benign

0.34

.;N;.;.

MutationTaster

Benign

1.0

P;P;P;P;P

PrimateAI

Benign

0.44

PROVEAN

Benign

-0.49

N;N;N;N

REVEL

Benign

0.016

Sift

Benign

0.63

T;T;T;T

Sift4G

Benign

0.24

T;T;T;T

Polyphen

0.0030

B;B;.;.

Vest4

0.087

MutPred

0.20

.;Loss of ubiquitination at K272 (P = 0.1264);Loss of ubiquitination at K272 (P = 0.1264);.;

MPC

0.39

ClinPred

0.0031

GERP RS

-1.1

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Varity_R

0.025

gMVP

0.058

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over