Variant rs130071 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_001105564.2(CCHCR1):c.1552C>T(p.Leu518Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.276 in 1,608,940 control chromosomes in the GnomAD database, including 63,886 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 0.25 ( 4991 hom., cov: 32)

Exomes 𝑓: 0.28 ( 58895 hom. )

Consequence

CCHCR1
NM_001105564.2 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.233

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 -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.5).

BP7

Synonymous conserved (PhyloP=-0.233 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.284 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCHCR1	NM_001105564.2 link	c.1552C>T	p.Leu518Leu	synonymous_variant	10/18	ENST00000396268.8	NP_001099034.1	Q8TD31-2Q769H0Q2TB68

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCHCR1	ENST00000396268.8 link	c.1552C>T	p.Leu518Leu	synonymous_variant	10/18	1	NM_001105564.2	ENSP00000379566.3		Q8TD31-2

Frequencies

GnomAD3 genomes

AF:

0.252

AC:

38269

AN:

151902

Hom.:

4991

Cov.:

show subpopulations

Gnomad AFR

AF:

0.201

Gnomad AMI

AF:

0.498

Gnomad AMR

AF:

0.248

Gnomad ASJ

AF:

0.373

Gnomad EAS

AF:

0.0626

Gnomad SAS

AF:

0.205

Gnomad FIN

AF:

0.276

Gnomad MID

AF:

0.363

Gnomad NFE

AF:

0.287

Gnomad OTH

AF:

0.275

GnomAD3 exomes

AF:

0.251

AC:

61811

AN:

245980

Hom.:

8433

AF XY:

0.253

AC XY:

33892

AN XY:

134070

show subpopulations

Gnomad AFR exome

AF:

0.204

Gnomad AMR exome

AF:

0.260

Gnomad ASJ exome

AF:

0.387

Gnomad EAS exome

AF:

0.0560

Gnomad SAS exome

AF:

0.218

Gnomad FIN exome

AF:

0.263

Gnomad NFE exome

AF:

0.281

Gnomad OTH exome

AF:

0.263

GnomAD4 exome

AF:

0.278

AC:

405645

AN:

1456920

Hom.:

58895

Cov.:

AF XY:

0.277

AC XY:

200576

AN XY:

724916

show subpopulations

Gnomad4 AFR exome

AF:

0.196

Gnomad4 AMR exome

AF:

0.261

Gnomad4 ASJ exome

AF:

0.388

Gnomad4 EAS exome

AF:

0.0553

Gnomad4 SAS exome

AF:

0.218

Gnomad4 FIN exome

AF:

0.265

Gnomad4 NFE exome

AF:

0.292

Gnomad4 OTH exome

AF:

0.285

GnomAD4 genome

AF:

0.252

AC:

38283

AN:

152020

Hom.:

4991

Cov.:

AF XY:

0.249

AC XY:

18475

AN XY:

74330

show subpopulations

Gnomad4 AFR

AF:

0.202

Gnomad4 AMR

AF:

0.248

Gnomad4 ASJ

AF:

0.373

Gnomad4 EAS

AF:

0.0627

Gnomad4 SAS

AF:

0.205

Gnomad4 FIN

AF:

0.276

Gnomad4 NFE

AF:

0.287

Gnomad4 OTH

AF:

0.273

Alfa

AF:

0.280

Hom.:

8474

Bravo

AF:

0.249

Asia WGS

AF:

0.146

AC:

512

AN:

3478

EpiCase

AF:

0.299

EpiControl

AF:

0.298

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.50

CADD

Benign

6.0

DANN

Benign

0.50

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