dbSNP rs6590113: CCDC15:p.Glu690Glu (chr11-124992618-A-G) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_025004.3(CCDC15):c.2070A>G(p.Glu690Glu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.21 in 1,594,302 control chromosomes in the GnomAD database, including 39,007 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 0.27 ( 6412 hom., cov: 32)

Exomes 𝑓: 0.20 ( 32595 hom. )

Consequence

CCDC15
NM_025004.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0260

Publications

15 publications found

Variant links:

Genes affected

CCDC15 (HGNC:25798): (coiled-coil domain containing 15) Located in centrosome. [provided by Alliance of Genome Resources, Apr 2022]

CCDC15 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.94).

BP7

Synonymous conserved (PhyloP=0.026 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.437 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC15	NM_025004.3 link	c.2070A>G	p.Glu690Glu	synonymous_variant	Exon 10 of 16	ENST00000344762.6	NP_079280.2	Q0P6D6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC15	ENST00000344762.6 link	c.2070A>G	p.Glu690Glu	synonymous_variant	Exon 10 of 16	5	NM_025004.3	ENSP00000341684.5		Q0P6D6
CCDC15	ENST00000529051.5 link	c.2070A>G	p.Glu690Glu	synonymous_variant	Exon 10 of 16	5		ENSP00000435403.1		E9PKB1

Frequencies

GnomAD3 genomes

AF:

0.267

AC:

40518

AN:

151960

Hom.:

6399

Cov.:

show subpopulations

Gnomad AFR

AF:

0.442

Gnomad AMI

AF:

0.239

Gnomad AMR

AF:

0.199

Gnomad ASJ

AF:

0.331

Gnomad EAS

AF:

0.189

Gnomad SAS

AF:

0.277

Gnomad FIN

AF:

0.178

Gnomad MID

AF:

0.268

Gnomad NFE

AF:

0.191

Gnomad OTH

AF:

0.266

GnomAD2 exomes

AF:

0.220

AC:

50364

AN:

229112

AF XY:

0.219

show subpopulations

Gnomad AFR exome

AF:

0.447

Gnomad AMR exome

AF:

0.181

Gnomad ASJ exome

AF:

0.305

Gnomad EAS exome

AF:

0.195

Gnomad FIN exome

AF:

0.172

Gnomad NFE exome

AF:

0.195

Gnomad OTH exome

AF:

0.221

GnomAD4 exome

AF:

0.204

AC:

294662

AN:

1442224

Hom.:

32595

Cov.:

AF XY:

0.206

AC XY:

147182

AN XY:

716082

show subpopulations

African (AFR)

AF:

0.451

AC:

14909

AN:

33022

American (AMR)

AF:

0.184

AC:

7896

AN:

42858

Ashkenazi Jewish (ASJ)

AF:

0.313

AC:

8045

AN:

25670

East Asian (EAS)

AF:

0.200

AC:

7857

AN:

39368

South Asian (SAS)

AF:

0.262

AC:

21778

AN:

83088

European-Finnish (FIN)

AF:

0.175

AC:

9235

AN:

52666

Middle Eastern (MID)

AF:

0.261

AC:

1499

AN:

5742

European-Non Finnish (NFE)

AF:

0.191

AC:

210035

AN:

1100068

Other (OTH)

AF:

0.224

AC:

13408

AN:

59742

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.441

Heterozygous variant carriers

10364

20728

31091

41455

51819

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

7542

15084

22626

30168

37710

<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:

0.267

AC:

40559

AN:

152078

Hom.:

6412

Cov.:

AF XY:

0.263

AC XY:

19553

AN XY:

74344

show subpopulations

African (AFR)

AF:

0.442

AC:

18321

AN:

41428

American (AMR)

AF:

0.199

AC:

3041

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.331

AC:

1148

AN:

3472

East Asian (EAS)

AF:

0.190

AC:

984

AN:

5184

South Asian (SAS)

AF:

0.276

AC:

1331

AN:

4816

European-Finnish (FIN)

AF:

0.178

AC:

1884

AN:

10572

Middle Eastern (MID)

AF:

0.260

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.191

AC:

13000

AN:

68000

Other (OTH)

AF:

0.263

AC:

556

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1415

2830

4244

5659

7074

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

400

800

1200

1600

2000

<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:

0.229

Hom.:

2023

Bravo

AF:

0.278

Asia WGS

AF:

0.244

AC:

849

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

0.28

(source)

DANN

Benign

0.34

PhyloP100

0.026

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.13

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