dbSNP rs130071: CCHCR1:p.Leu518Leu (chr6-31148433-G-A) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -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

Publications

30 publications found

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 was made for transcript

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CCHCR1	NM_001105564.2 link	c.1552C>T	p.Leu518Leu	synonymous_variant	Exon 10 of 18	ENST00000396268.8	NP_001099034.1	Q8TD31-2Q769H0Q2TB68

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCHCR1	ENST00000396268.8 link	c.1552C>T	p.Leu518Leu	synonymous_variant	Exon 10 of 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

GnomAD2 exomes

AF:

0.251

AC:

61811

AN:

245980

AF XY:

0.253

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 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

African (AFR)

AF:

0.196

AC:

6556

AN:

33402

American (AMR)

AF:

0.261

AC:

11635

AN:

44654

Ashkenazi Jewish (ASJ)

AF:

0.388

AC:

10109

AN:

26078

East Asian (EAS)

AF:

0.0553

AC:

2195

AN:

39694

South Asian (SAS)

AF:

0.218

AC:

18796

AN:

86108

European-Finnish (FIN)

AF:

0.265

AC:

13851

AN:

52302

Middle Eastern (MID)

AF:

0.302

AC:

1741

AN:

5758

European-Non Finnish (NFE)

AF:

0.292

AC:

323572

AN:

1108672

Other (OTH)

AF:

0.285

AC:

17190

AN:

60252

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.481

Heterozygous variant carriers

13416

26832

40249

53665

67081

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.252

AC:

38283

AN:

152020

Hom.:

4991

Cov.:

AF XY:

0.249

AC XY:

18475

AN XY:

74330

show subpopulations

African (AFR)

AF:

0.202

AC:

8354

AN:

41454

American (AMR)

AF:

0.248

AC:

3783

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.373

AC:

1293

AN:

3470

East Asian (EAS)

AF:

0.0627

AC:

324

AN:

5166

South Asian (SAS)

AF:

0.205

AC:

988

AN:

4828

European-Finnish (FIN)

AF:

0.276

AC:

2916

AN:

10576

Middle Eastern (MID)

AF:

0.349

AC:

102

AN:

292

European-Non Finnish (NFE)

AF:

0.287

AC:

19497

AN:

67938

Other (OTH)

AF:

0.273

AC:

576

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1468

2936

4405

5873

7341

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.273

Hom.:

19406

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

(source)

DANN

Benign

0.50

PhyloP100

-0.23

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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rs130071

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over