Genetic Variant CCDC152:c.194-52T>C (chr5-42769545-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001134848.2(CCDC152):c.194-52T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.26 in 1,411,194 control chromosomes in the GnomAD database, including 50,444 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 0.22 ( 4520 hom., cov: 32)

Exomes 𝑓: 0.27 ( 45924 hom. )

Consequence

CCDC152
NM_001134848.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.60

Publications

15 publications found

Variant links:

Genes affected

CCDC152 (HGNC:34438): (coiled-coil domain containing 152)

CCDC152 links:

Genome browser will be placed here

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=-0.52).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.34 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC152	NM_001134848.2 link	c.194-52T>C		intron_variant	Intron 3 of 8	ENST00000361970.10	NP_001128320.1	Q4G0S7-1A0A024R043
CCDC152	XM_047416584.1 link	c.257-52T>C		intron_variant	Intron 3 of 8		XP_047272540.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC152	ENST00000361970.10 link	c.194-52T>C		intron_variant	Intron 3 of 8	1	NM_001134848.2	ENSP00000354888.5		Q4G0S7-1
CCDC152	ENST00000388827.4 link	c.194-52T>C		intron_variant	Intron 3 of 6	2		ENSP00000373479.4		Q4G0S7-2

Frequencies

GnomAD3 genomes

AF:

0.219

AC:

33189

AN:

151852

Hom.:

4510

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0609

Gnomad AMI

AF:

0.225

Gnomad AMR

AF:

0.347

Gnomad ASJ

AF:

0.249

Gnomad EAS

AF:

0.259

Gnomad SAS

AF:

0.200

Gnomad FIN

AF:

0.332

Gnomad MID

AF:

0.114

Gnomad NFE

AF:

0.266

Gnomad OTH

AF:

0.209

GnomAD4 exome

AF:

0.265

AC:

334095

AN:

1259224

Hom.:

45924

AF XY:

0.263

AC XY:

162915

AN XY:

618326

show subpopulations

African (AFR)

AF:

0.0505

AC:

1322

AN:

26184

American (AMR)

AF:

0.407

AC:

7010

AN:

17218

Ashkenazi Jewish (ASJ)

AF:

0.249

AC:

5328

AN:

21370

East Asian (EAS)

AF:

0.299

AC:

9209

AN:

30780

South Asian (SAS)

AF:

0.205

AC:

13506

AN:

65884

European-Finnish (FIN)

AF:

0.328

AC:

13538

AN:

41300

Middle Eastern (MID)

AF:

0.165

AC:

800

AN:

4860

European-Non Finnish (NFE)

AF:

0.271

AC:

271006

AN:

1000228

Other (OTH)

AF:

0.241

AC:

12376

AN:

51400

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.481

Heterozygous variant carriers

11323

22646

33968

45291

56614

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

9464

18928

28392

37856

47320

<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:

0.219

AC:

33227

AN:

151970

Hom.:

4520

Cov.:

AF XY:

0.222

AC XY:

16508

AN XY:

74326

show subpopulations

African (AFR)

AF:

0.0608

AC:

2524

AN:

41510

American (AMR)

AF:

0.347

AC:

5308

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.249

AC:

864

AN:

3468

East Asian (EAS)

AF:

0.260

AC:

1346

AN:

5168

South Asian (SAS)

AF:

0.200

AC:

968

AN:

4828

European-Finnish (FIN)

AF:

0.332

AC:

3468

AN:

10460

Middle Eastern (MID)

AF:

0.126

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.266

AC:

18053

AN:

67942

Other (OTH)

AF:

0.215

AC:

454

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1229

2458

3688

4917

6146

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

356

712

1068

1424

1780

<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:

0.234

Hom.:

632

Bravo

AF:

0.214

Asia WGS

AF:

0.220

AC:

762

AN:

3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.52

CADD

Benign

(source)

DANN

Benign

0.80

PhyloP100

1.6

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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