dbSNP rs11967883: CCHCR1:c.2167+110G>A (chr6-31144577-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001105564.2(CCHCR1):c.2167+110G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.047 in 713,482 control chromosomes in the GnomAD database, including 1,587 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 0.064 ( 514 hom., cov: 31)

Exomes 𝑓: 0.042 ( 1073 hom. )

Consequence

CCHCR1
NM_001105564.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.02

Publications

5 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 -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.158 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001105564.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
CCHCR1	NM_001105564.2	MANE Select	c.2167+110G>A	intron	N/A	NP_001099034.1	Q8TD31-2
CCHCR1	NM_001394641.1		c.2194+110G>A	intron	N/A	NP_001381570.1
CCHCR1	NM_001105563.3		c.2059+110G>A	intron	N/A	NP_001099033.1	Q8TD31-3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
CCHCR1	ENST00000396268.8	TSL:1 MANE Select	c.2167+110G>A	intron	N/A	ENSP00000379566.3	Q8TD31-2
CCHCR1	ENST00000451521.6	TSL:1	c.2059+110G>A	intron	N/A	ENSP00000401039.2	Q8TD31-3
CCHCR1	ENST00000376266.9	TSL:1	c.1900+110G>A	intron	N/A	ENSP00000365442.5	Q8TD31-1

Frequencies

GnomAD3 genomes

AF:

0.0638

AC:

9703

AN:

152008

Hom.:

512

Cov.:

show subpopulations

Gnomad AFR

AF:

0.137

Gnomad AMI

AF:

0.0220

Gnomad AMR

AF:

0.0338

Gnomad ASJ

AF:

0.0268

Gnomad EAS

AF:

0.168

Gnomad SAS

AF:

0.0415

Gnomad FIN

AF:

0.0527

Gnomad MID

AF:

0.0191

Gnomad NFE

AF:

0.0241

Gnomad OTH

AF:

0.0636

GnomAD4 exome

AF:

0.0425

AC:

23849

AN:

561356

Hom.:

1073

Cov.:

AF XY:

0.0408

AC XY:

12103

AN XY:

296318

show subpopulations

African (AFR)

AF:

0.140

AC:

2160

AN:

15380

American (AMR)

AF:

0.0263

AC:

750

AN:

28480

Ashkenazi Jewish (ASJ)

AF:

0.0273

AC:

413

AN:

15146

East Asian (EAS)

AF:

0.186

AC:

6511

AN:

35014

South Asian (SAS)

AF:

0.0360

AC:

1922

AN:

53366

European-Finnish (FIN)

AF:

0.0593

AC:

2171

AN:

36594

Middle Eastern (MID)

AF:

0.0322

AC:

110

AN:

3412

European-Non Finnish (NFE)

AF:

0.0243

AC:

8363

AN:

343908

Other (OTH)

AF:

0.0482

AC:

1449

AN:

30056

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.514

Heterozygous variant carriers

1205

2410

3616

4821

6026

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

218

436

654

872

1090

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0638

AC:

9707

AN:

152126

Hom.:

514

Cov.:

AF XY:

0.0650

AC XY:

4832

AN XY:

74370

show subpopulations

African (AFR)

AF:

0.137

AC:

5676

AN:

41482

American (AMR)

AF:

0.0338

AC:

517

AN:

15300

Ashkenazi Jewish (ASJ)

AF:

0.0268

AC:

AN:

3468

East Asian (EAS)

AF:

0.167

AC:

864

AN:

5166

South Asian (SAS)

AF:

0.0416

AC:

200

AN:

4812

European-Finnish (FIN)

AF:

0.0527

AC:

558

AN:

10592

Middle Eastern (MID)

AF:

0.0171

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.0241

AC:

1638

AN:

67992

Other (OTH)

AF:

0.0644

AC:

136

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.512

Heterozygous variant carriers

447

893

1340

1786

2233

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

114

228

342

456

570

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0371

Hom.:

474

Bravo

AF:

0.0671

Asia WGS

AF:

0.114

AC:

394

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

6.7

(source)

DANN

Benign

0.66

PhyloP100

1.0

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over