Genetic Variant CCHCR1:n.1999C>G (chr6-31144825-G-C) – 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.1999C>G 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 0.304 in 1,607,840 control chromosomes in the GnomAD database, including 76,992 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 0.28 ( 6184 hom., cov: 30)

Exomes 𝑓: 0.31 ( 70808 hom. )

Consequence

CCHCR1
ENST00000509552.5 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.620

Publications

33 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=-0.89).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.314 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCHCR1	NM_001105564.2 link	c.2066-37C>G		intron_variant	Intron 14 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.2066-37C>G		intron_variant	Intron 14 of 17	1	NM_001105564.2	ENSP00000379566.3		Q8TD31-2

Frequencies

GnomAD3 genomes

AF:

0.281

AC:

42642

AN:

151758

Hom.:

6185

Cov.:

show subpopulations

Gnomad AFR

AF:

0.230

Gnomad AMI

AF:

0.518

Gnomad AMR

AF:

0.265

Gnomad ASJ

AF:

0.416

Gnomad EAS

AF:

0.0836

Gnomad SAS

AF:

0.220

Gnomad FIN

AF:

0.317

Gnomad MID

AF:

0.414

Gnomad NFE

AF:

0.318

Gnomad OTH

AF:

0.306

GnomAD2 exomes

AF:

0.279

AC:

69989

AN:

251150

AF XY:

0.280

show subpopulations

Gnomad AFR exome

AF:

0.234

Gnomad AMR exome

AF:

0.275

Gnomad ASJ exome

AF:

0.439

Gnomad EAS exome

AF:

0.0771

Gnomad FIN exome

AF:

0.302

Gnomad NFE exome

AF:

0.311

Gnomad OTH exome

AF:

0.294

GnomAD4 exome

AF:

0.306

AC:

446073

AN:

1455964

Hom.:

70808

Cov.:

AF XY:

0.305

AC XY:

220758

AN XY:

724412

show subpopulations

African (AFR)

AF:

0.228

AC:

7625

AN:

33398

American (AMR)

AF:

0.277

AC:

12364

AN:

44694

Ashkenazi Jewish (ASJ)

AF:

0.440

AC:

11476

AN:

26092

East Asian (EAS)

AF:

0.0681

AC:

2698

AN:

39628

South Asian (SAS)

AF:

0.237

AC:

20409

AN:

86114

European-Finnish (FIN)

AF:

0.302

AC:

16073

AN:

53292

Middle Eastern (MID)

AF:

0.335

AC:

1929

AN:

5756

European-Non Finnish (NFE)

AF:

0.320

AC:

354605

AN:

1106802

Other (OTH)

AF:

0.314

AC:

18894

AN:

60188

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

17082

34164

51245

68327

85409

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

11482

22964

34446

45928

57410

<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:

0.281

AC:

42659

AN:

151876

Hom.:

6184

Cov.:

AF XY:

0.278

AC XY:

20619

AN XY:

74194

show subpopulations

African (AFR)

AF:

0.230

AC:

9544

AN:

41428

American (AMR)

AF:

0.264

AC:

4034

AN:

15258

Ashkenazi Jewish (ASJ)

AF:

0.416

AC:

1444

AN:

3470

East Asian (EAS)

AF:

0.0838

AC:

432

AN:

5158

South Asian (SAS)

AF:

0.219

AC:

1052

AN:

4804

European-Finnish (FIN)

AF:

0.317

AC:

3341

AN:

10528

Middle Eastern (MID)

AF:

0.404

AC:

118

AN:

292

European-Non Finnish (NFE)

AF:

0.318

AC:

21582

AN:

67916

Other (OTH)

AF:

0.303

AC:

640

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1561

3123

4684

6246

7807

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

440

880

1320

1760

2200

<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:

0.316

Hom.:

1596

Bravo

AF:

0.279

Asia WGS

AF:

0.158

AC:

551

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

4.9

(source)

DANN

Benign

0.60

PhyloP100

-0.62

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