dbSNP rs1265074: CCHCR1:c.1739+11G>T (chr6-31145437-C-A) – 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.1739+11G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.206 in 1,613,692 control chromosomes in the GnomAD database, including 35,959 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 0.21 ( 3496 hom., cov: 33)

Exomes 𝑓: 0.21 ( 32463 hom. )

Consequence

CCHCR1
NM_001105564.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.848

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 -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.7).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.328 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCHCR1	NM_001105564.2 link	c.1739+11G>T		intron_variant	Intron 12 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.1739+11G>T		intron_variant	Intron 12 of 17	1	NM_001105564.2	ENSP00000379566.3		Q8TD31-2

Frequencies

GnomAD3 genomes

AF:

0.210

AC:

31951

AN:

151978

Hom.:

3495

Cov.:

show subpopulations

Gnomad AFR

AF:

0.195

Gnomad AMI

AF:

0.104

Gnomad AMR

AF:

0.286

Gnomad ASJ

AF:

0.107

Gnomad EAS

AF:

0.341

Gnomad SAS

AF:

0.245

Gnomad FIN

AF:

0.224

Gnomad MID

AF:

0.190

Gnomad NFE

AF:

0.195

Gnomad OTH

AF:

0.189

GnomAD2 exomes

AF:

0.228

AC:

57373

AN:

251426

AF XY:

0.225

show subpopulations

Gnomad AFR exome

AF:

0.192

Gnomad AMR exome

AF:

0.313

Gnomad ASJ exome

AF:

0.0982

Gnomad EAS exome

AF:

0.334

Gnomad FIN exome

AF:

0.232

Gnomad NFE exome

AF:

0.199

Gnomad OTH exome

AF:

0.217

GnomAD4 exome

AF:

0.206

AC:

300787

AN:

1461596

Hom.:

32463

Cov.:

AF XY:

0.206

AC XY:

149482

AN XY:

727114

show subpopulations

African (AFR)

AF:

0.191

AC:

6378

AN:

33476

American (AMR)

AF:

0.309

AC:

13814

AN:

44722

Ashkenazi Jewish (ASJ)

AF:

0.103

AC:

2679

AN:

26136

East Asian (EAS)

AF:

0.340

AC:

13483

AN:

39700

South Asian (SAS)

AF:

0.243

AC:

20998

AN:

86250

European-Finnish (FIN)

AF:

0.229

AC:

12233

AN:

53420

Middle Eastern (MID)

AF:

0.199

AC:

1141

AN:

5748

European-Non Finnish (NFE)

AF:

0.196

AC:

218365

AN:

1111756

Other (OTH)

AF:

0.194

AC:

11696

AN:

60388

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.479

Heterozygous variant carriers

13188

26375

39563

52750

65938

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

7784

15568

23352

31136

38920

<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:

0.210

AC:

31966

AN:

152096

Hom.:

3496

Cov.:

AF XY:

0.214

AC XY:

15913

AN XY:

74360

show subpopulations

African (AFR)

AF:

0.195

AC:

8083

AN:

41464

American (AMR)

AF:

0.286

AC:

4377

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.107

AC:

373

AN:

3472

East Asian (EAS)

AF:

0.341

AC:

1763

AN:

5164

South Asian (SAS)

AF:

0.243

AC:

1175

AN:

4826

European-Finnish (FIN)

AF:

0.224

AC:

2373

AN:

10586

Middle Eastern (MID)

AF:

0.190

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.195

AC:

13268

AN:

67986

Other (OTH)

AF:

0.192

AC:

403

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1286

2572

3857

5143

6429

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

352

704

1056

1408

1760

<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:

0.197

Hom.:

5521

Bravo

AF:

0.214

Asia WGS

AF:

0.312

AC:

1083

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.70

CADD

Benign

(source)

DANN

Benign

0.84

PhyloP100

0.85

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.060

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