Genetic Variant CCDC201:c.271-5857T>C (chr7-45873165-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The XM_047419863.1(CCDC201):c.271-5857T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.831 in 152,310 control chromosomes in the GnomAD database, including 53,257 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 0.83 ( 53197 hom., cov: 31)

Exomes 𝑓: 0.79 ( 60 hom. )

Consequence

CCDC201
XM_047419863.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.275

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=-0.93).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.946 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC201	XM_047419863.1 link	c.271-5857T>C		intron_variant	Intron 1 of 3		XP_047275819.1
CCDC201	NM_001395235.1 link	c.-158T>C		upstream_gene_variant		ENST00000636578.2	NP_001382164.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC201	ENST00000636578.2 link	c.-158T>C		upstream_gene_variant		5	NM_001395235.1	ENSP00000489712.1		A0A1B0GTI1

Frequencies

GnomAD3 genomes

AF:

0.831

AC:

126371

AN:

152010

Hom.:

53144

Cov.:

show subpopulations

Gnomad AFR

AF:

0.954

Gnomad AMI

AF:

0.774

Gnomad AMR

AF:

0.807

Gnomad ASJ

AF:

0.776

Gnomad EAS

AF:

0.902

Gnomad SAS

AF:

0.610

Gnomad FIN

AF:

0.870

Gnomad MID

AF:

0.756

Gnomad NFE

AF:

0.770

Gnomad OTH

AF:

0.829

GnomAD4 exome

AF:

0.786

AC:

143

AN:

182

Hom.:

AF XY:

0.764

AC XY:

113

AN XY:

148

show subpopulations

African (AFR)

AF:

1.00

AC:

AN:

American (AMR)

AF:

0.500

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.250

AC:

AN:

East Asian (EAS)

AF:

1.00

AC:

AN:

South Asian (SAS)

AF:

0.500

AC:

AN:

European-Finnish (FIN)

AF:

1.00

AC:

AN:

Middle Eastern (MID)

AF:

1.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.785

AC:

113

AN:

144

Other (OTH)

AF:

0.875

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

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:

0.831

AC:

126485

AN:

152128

Hom.:

53197

Cov.:

AF XY:

0.832

AC XY:

61889

AN XY:

74358

show subpopulations

African (AFR)

AF:

0.954

AC:

39618

AN:

41524

American (AMR)

AF:

0.807

AC:

12333

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.776

AC:

2693

AN:

3472

East Asian (EAS)

AF:

0.902

AC:

4642

AN:

5144

South Asian (SAS)

AF:

0.610

AC:

2939

AN:

4820

European-Finnish (FIN)

AF:

0.870

AC:

9216

AN:

10592

Middle Eastern (MID)

AF:

0.759

AC:

220

AN:

290

European-Non Finnish (NFE)

AF:

0.770

AC:

52372

AN:

67976

Other (OTH)

AF:

0.827

AC:

1746

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

1055

2111

3166

4222

5277

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

874

1748

2622

3496

4370

<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:

0.778

Hom.:

82894

Bravo

AF:

0.839

Asia WGS

AF:

0.764

AC:

2658

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

1.2

(source)

DANN

Benign

0.53

PhyloP100

-0.28

PromoterAI

0.064

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