Variant chr6-31144707-C-T details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001105564.2(CCHCR1):c.2147G>A(p.Arg716Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0799 in 1,610,764 control chromosomes in the GnomAD database, including 6,066 homozygotes. 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: 𝑓 0.085 ( 662 hom., cov: 31)

Exomes 𝑓: 0.079 ( 5404 hom. )

Consequence

CCHCR1
NM_001105564.2 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.96

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=0.0021642745).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.113 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.2147G>A	p.Arg716Gln	missense_variant	15/18	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.2147G>A	p.Arg716Gln	missense_variant	15/18	1	NM_001105564.2	ENSP00000379566	A2	Q8TD31-2

Frequencies

GnomAD3 genomes

AF:

0.0847

AC:

12884

AN:

152080

Hom.:

662

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0499

Gnomad AMI

AF:

0.173

Gnomad AMR

AF:

0.117

Gnomad ASJ

AF:

0.132

Gnomad EAS

AF:

0.0426

Gnomad SAS

AF:

0.0942

Gnomad FIN

AF:

0.180

Gnomad MID

AF:

0.161

Gnomad NFE

AF:

0.0817

Gnomad OTH

AF:

0.111

GnomAD3 exomes

AF:

0.102

AC:

25424

AN:

250152

Hom.:

1528

AF XY:

0.102

AC XY:

13748

AN XY:

135128

show subpopulations

Gnomad AFR exome

AF:

0.0515

Gnomad AMR exome

AF:

0.159

Gnomad ASJ exome

AF:

0.140

Gnomad EAS exome

AF:

0.0452

Gnomad SAS exome

AF:

0.0963

Gnomad FIN exome

AF:

0.167

Gnomad NFE exome

AF:

0.0865

Gnomad OTH exome

AF:

0.0949

GnomAD4 exome

AF:

0.0794

AC:

115815

AN:

1458566

Hom.:

5404

Cov.:

AF XY:

0.0804

AC XY:

58290

AN XY:

725136

show subpopulations

Gnomad4 AFR exome

AF:

0.0499

Gnomad4 AMR exome

AF:

0.156

Gnomad4 ASJ exome

AF:

0.137

Gnomad4 EAS exome

AF:

0.0460

Gnomad4 SAS exome

AF:

0.0991

Gnomad4 FIN exome

AF:

0.163

Gnomad4 NFE exome

AF:

0.0711

Gnomad4 OTH exome

AF:

0.0838

GnomAD4 genome

AF:

0.0847

AC:

12894

AN:

152198

Hom.:

662

Cov.:

AF XY:

0.0891

AC XY:

6634

AN XY:

74416

show subpopulations

Gnomad4 AFR

AF:

0.0499

Gnomad4 AMR

AF:

0.117

Gnomad4 ASJ

AF:

0.132

Gnomad4 EAS

AF:

0.0427

Gnomad4 SAS

AF:

0.0942

Gnomad4 FIN

AF:

0.180

Gnomad4 NFE

AF:

0.0817

Gnomad4 OTH

AF:

0.112

Alfa

AF:

0.0862

Hom.:

1321

Bravo

AF:

0.0804

TwinsUK

AF:

0.0623

AC:

231

ALSPAC

AF:

0.0667

AC:

257

ESP6500AA

AF:

0.0531

AC:

234

ESP6500EA

AF:

0.0867

AC:

746

ExAC

AF:

0.0974

AC:

11819

Asia WGS

AF:

0.0780

AC:

272

AN:

3478

EpiCase

AF:

0.0959

EpiControl

AF:

0.104

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.10

BayesDel_addAF

Benign

-0.56

BayesDel_noAF

Benign

-0.43

CADD

Uncertain

DANN

Pathogenic

1.0

DEOGEN2

Benign

0.017

.;T;T;.

Eigen

Uncertain

0.44

Eigen_PC

Uncertain

0.38

FATHMM_MKL

Uncertain

0.89

LIST_S2

Benign

0.82

.;.;.;T

MetaRNN

Benign

0.0022

T;T;T;T

MetaSVM

Benign

-1.1

MutationAssessor

Uncertain

2.2

.;M;.;.

MutationTaster

Benign

0.66

P;P;P;P;P

PrimateAI

Benign

0.45

PROVEAN

Benign

-1.7

N;N;N;N

REVEL

Benign

0.083

Sift

Uncertain

0.0030

D;D;D;D

Sift4G

Benign

0.19

T;T;T;T

Polyphen

1.0

D;D;.;.

Vest4

0.25

MPC

0.83

ClinPred

0.012

GERP RS

4.2

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Varity_R

0.033

gMVP

0.43

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