Variant 6-31157072-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_001105564.2(CCHCR1):c.234G>A(p.Trp78Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.481 in 1,608,130 control chromosomes in the GnomAD database, including 187,598 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Variant results in nonsense mediated mRNA decay.

Frequency

Genomes: 𝑓 0.48 ( 17722 hom., cov: 32)

Exomes 𝑓: 0.48 ( 169876 hom. )

Consequence

CCHCR1
NM_001105564.2 stop_gained

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.265

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 -8 ACMG points.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.502 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.234G>A	p.Trp78Ter	stop_gained	2/18	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.234G>A	p.Trp78Ter	stop_gained	2/18	1	NM_001105564.2	ENSP00000379566	A2	Q8TD31-2

Frequencies

GnomAD3 genomes

AF:

0.481

AC:

73061

AN:

151904

Hom.:

17717

Cov.:

show subpopulations

Gnomad AFR

AF:

0.495

Gnomad AMI

AF:

0.477

Gnomad AMR

AF:

0.512

Gnomad ASJ

AF:

0.607

Gnomad EAS

AF:

0.393

Gnomad SAS

AF:

0.461

Gnomad FIN

AF:

0.401

Gnomad MID

AF:

0.563

Gnomad NFE

AF:

0.480

Gnomad OTH

AF:

0.469

GnomAD3 exomes

AF:

0.468

AC:

114039

AN:

243836

Hom.:

27029

AF XY:

0.468

AC XY:

62211

AN XY:

132990

show subpopulations

Gnomad AFR exome

AF:

0.492

Gnomad AMR exome

AF:

0.477

Gnomad ASJ exome

AF:

0.597

Gnomad EAS exome

AF:

0.377

Gnomad SAS exome

AF:

0.466

Gnomad FIN exome

AF:

0.406

Gnomad NFE exome

AF:

0.477

Gnomad OTH exome

AF:

0.485

GnomAD4 exome

AF:

0.481

AC:

700088

AN:

1456108

Hom.:

169876

Cov.:

AF XY:

0.480

AC XY:

348003

AN XY:

724352

show subpopulations

Gnomad4 AFR exome

AF:

0.499

Gnomad4 AMR exome

AF:

0.481

Gnomad4 ASJ exome

AF:

0.597

Gnomad4 EAS exome

AF:

0.371

Gnomad4 SAS exome

AF:

0.471

Gnomad4 FIN exome

AF:

0.403

Gnomad4 NFE exome

AF:

0.485

Gnomad4 OTH exome

AF:

0.485

GnomAD4 genome

AF:

0.481

AC:

73091

AN:

152022

Hom.:

17722

Cov.:

AF XY:

0.477

AC XY:

35411

AN XY:

74310

show subpopulations

Gnomad4 AFR

AF:

0.495

Gnomad4 AMR

AF:

0.511

Gnomad4 ASJ

AF:

0.607

Gnomad4 EAS

AF:

0.394

Gnomad4 SAS

AF:

0.458

Gnomad4 FIN

AF:

0.401

Gnomad4 NFE

AF:

0.480

Gnomad4 OTH

AF:

0.469

Alfa

AF:

0.483

Hom.:

38428

Bravo

AF:

0.490

TwinsUK

AF:

0.496

AC:

1840

ALSPAC

AF:

0.482

AC:

1857

ESP6500AA

AF:

0.491

AC:

1483

ESP6500EA

AF:

0.482

AC:

2610

ExAC

AF:

0.465

AC:

54539

Asia WGS

AF:

0.451

AC:

1566

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Uncertain

0.13

BayesDel_noAF

Pathogenic

0.56

CADD

Pathogenic

DANN

Uncertain

0.99

Eigen

Uncertain

0.68

Eigen_PC

Uncertain

0.50

FATHMM_MKL

Benign

0.34

MutationTaster

Benign

1.9e-20

P;P;P;P;P

Vest4

0.86

GERP RS

3.7

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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