Genetic Variant CCDC201:c.18+125G>C (chr7-45872865-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001395235.1(CCDC201):c.18+125G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.279 in 152,820 control chromosomes in the GnomAD database, including 6,220 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 ( 6189 hom., cov: 33)

Exomes 𝑓: 0.26 ( 31 hom. )

Consequence

CCDC201
NM_001395235.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.64

Publications

7 publications found

Variant links:

Genes affected

CCDC201 (HGNC:54081): (coiled-coil domain containing 201)

CCDC201 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=-0.83).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.307 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC201	NM_001395235.1 link	c.18+125G>C		intron_variant	Intron 1 of 2	ENST00000636578.2	NP_001382164.1
CCDC201	XM_047419863.1 link	c.271-5557G>C		intron_variant	Intron 1 of 3		XP_047275819.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC201	ENST00000636578.2 link	c.18+125G>C		intron_variant	Intron 1 of 2	5	NM_001395235.1	ENSP00000489712.1

Frequencies

GnomAD3 genomes

AF:

0.279

AC:

42393

AN:

151988

Hom.:

6181

Cov.:

show subpopulations

Gnomad AFR

AF:

0.311

Gnomad AMI

AF:

0.323

Gnomad AMR

AF:

0.287

Gnomad ASJ

AF:

0.194

Gnomad EAS

AF:

0.270

Gnomad SAS

AF:

0.197

Gnomad FIN

AF:

0.428

Gnomad MID

AF:

0.215

Gnomad NFE

AF:

0.245

Gnomad OTH

AF:

0.270

GnomAD4 exome

AF:

0.256

AC:

183

AN:

714

Hom.:

AF XY:

0.257

AC XY:

136

AN XY:

530

show subpopulations

African (AFR)

AF:

0.357

AC:

AN:

American (AMR)

AF:

0.250

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AF:

0.250

AC:

AN:

South Asian (SAS)

AF:

0.125

AC:

AN:

European-Finnish (FIN)

AF:

0.556

AC:

AN:

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.257

AC:

157

AN:

610

Other (OTH)

AF:

0.0769

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.491

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<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:

0.279

AC:

42429

AN:

152106

Hom.:

6189

Cov.:

AF XY:

0.286

AC XY:

21262

AN XY:

74316

show subpopulations

African (AFR)

AF:

0.311

AC:

12907

AN:

41502

American (AMR)

AF:

0.287

AC:

4389

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.194

AC:

673

AN:

3470

East Asian (EAS)

AF:

0.271

AC:

1398

AN:

5164

South Asian (SAS)

AF:

0.197

AC:

952

AN:

4826

European-Finnish (FIN)

AF:

0.428

AC:

4523

AN:

10576

Middle Eastern (MID)

AF:

0.235

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.245

AC:

16660

AN:

67958

Other (OTH)

AF:

0.267

AC:

564

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1577

3154

4732

6309

7886

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

428

856

1284

1712

2140

<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:

0.167

Hom.:

382

Bravo

AF:

0.268

Asia WGS

AF:

0.234

AC:

813

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

1.8

(source)

DANN

Benign

0.81

PhyloP100

-1.6

PromoterAI

-0.074

Neutral

(source)

Splicing

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