dbSNP rs11967883: CCHCR1:n.2247G>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 ENST00000509552.5(CCHCR1):n.2247G>A variant causes a non coding transcript exon 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
ENST00000509552.5 non_coding_transcript_exon

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCHCR1	NM_001105564.2 link	c.2167+110G>A		intron_variant	Intron 15 of 17	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.2167+110G>A		intron_variant	Intron 15 of 17	1	NM_001105564.2	ENSP00000379566.3		Q8TD31-2

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 v4.3

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over