Variant chr6-31148469-G-A 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.1516C>T(p.Arg506Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.443 in 1,611,098 control chromosomes in the GnomAD database, including 160,187 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 0.44 ( 14675 hom., cov: 32)

Exomes 𝑓: 0.44 ( 145512 hom. )

Consequence

CCHCR1
NM_001105564.2 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.209

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=1.5869737E-4).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.443 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.1516C>T	p.Arg506Trp	missense_variant	10/18	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.1516C>T	p.Arg506Trp	missense_variant	10/18	1	NM_001105564.2	ENSP00000379566	A2	Q8TD31-2

Frequencies

GnomAD3 genomes

AF:

0.439

AC:

66673

AN:

151924

Hom.:

14676

Cov.:

show subpopulations

Gnomad AFR

AF:

0.422

Gnomad AMI

AF:

0.582

Gnomad AMR

AF:

0.408

Gnomad ASJ

AF:

0.512

Gnomad EAS

AF:

0.292

Gnomad SAS

AF:

0.421

Gnomad FIN

AF:

0.527

Gnomad MID

AF:

0.608

Gnomad NFE

AF:

0.448

Gnomad OTH

AF:

0.467

GnomAD3 exomes

AF:

0.440

AC:

108347

AN:

246312

Hom.:

24533

AF XY:

0.445

AC XY:

59794

AN XY:

134264

show subpopulations

Gnomad AFR exome

AF:

0.424

Gnomad AMR exome

AF:

0.407

Gnomad ASJ exome

AF:

0.529

Gnomad EAS exome

AF:

0.296

Gnomad SAS exome

AF:

0.458

Gnomad FIN exome

AF:

0.512

Gnomad NFE exome

AF:

0.448

Gnomad OTH exome

AF:

0.460

GnomAD4 exome

AF:

0.443

AC:

647025

AN:

1459056

Hom.:

145512

Cov.:

AF XY:

0.445

AC XY:

323115

AN XY:

725864

show subpopulations

Gnomad4 AFR exome

AF:

0.419

Gnomad4 AMR exome

AF:

0.413

Gnomad4 ASJ exome

AF:

0.533

Gnomad4 EAS exome

AF:

0.289

Gnomad4 SAS exome

AF:

0.458

Gnomad4 FIN exome

AF:

0.514

Gnomad4 NFE exome

AF:

0.443

Gnomad4 OTH exome

AF:

0.461

GnomAD4 genome

AF:

0.439

AC:

66695

AN:

152042

Hom.:

14675

Cov.:

AF XY:

0.440

AC XY:

32713

AN XY:

74316

show subpopulations

Gnomad4 AFR

AF:

0.422

Gnomad4 AMR

AF:

0.408

Gnomad4 ASJ

AF:

0.512

Gnomad4 EAS

AF:

0.291

Gnomad4 SAS

AF:

0.420

Gnomad4 FIN

AF:

0.527

Gnomad4 NFE

AF:

0.448

Gnomad4 OTH

AF:

0.464

Alfa

AF:

0.453

Hom.:

24774

Bravo

AF:

0.434

TwinsUK

AF:

0.436

AC:

1617

ALSPAC

AF:

0.434

AC:

1674

ESP6500AA

AF:

0.434

AC:

1312

ESP6500EA

AF:

0.444

AC:

2408

ExAC

AF:

0.437

AC:

51479

Asia WGS

AF:

0.421

AC:

1468

AN:

3478

EpiCase

AF:

0.473

EpiControl

AF:

0.477

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.085

BayesDel_addAF

Benign

-0.70

BayesDel_noAF

Benign

-0.64

CADD

Benign

DANN

Benign

0.86

DEOGEN2

Benign

0.0065

.;T;T;.

Eigen

Benign

-1.1

Eigen_PC

Benign

-1.1

FATHMM_MKL

Benign

0.030

LIST_S2

Benign

0.78

.;.;.;T

MetaRNN

Benign

0.00016

T;T;T;T

MetaSVM

Benign

-0.93

MutationAssessor

Benign

1.4

.;L;.;.

MutationTaster

Benign

1.0

P;P;P;P;P

PrimateAI

Benign

0.36

PROVEAN

Benign

-0.73

N;N;N;N

REVEL

Benign

0.021

Sift

Benign

0.15

T;T;T;T

Sift4G

Benign

0.14

T;T;T;T

Polyphen

0.0030

B;B;.;.

Vest4

0.15

MPC

0.46

ClinPred

0.0053

GERP RS

1.1

Varity_R

0.12

gMVP

0.19

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