dbSNP rs2028414: CEP170B:p.Pro198Pro (chr14-104883051-A-C) – ACMG Classification: Benign (-14 pts)

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1

The NM_001112726.3(CEP170B):c.594A>C(p.Pro198Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.627 in 1,529,066 control chromosomes in the GnomAD database, including 306,830 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.59 ( 27392 hom., cov: 27)

Exomes 𝑓: 0.63 ( 279438 hom. )

Consequence

CEP170B
NM_001112726.3 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -1.83

Publications

28 publications found

Variant links:

Genes affected

CEP170B (HGNC:20362): (centrosomal protein 170B) Predicted to be located in cytoplasm and microtubule. [provided by Alliance of Genome Resources, Apr 2022]

CEP170B links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.99).

BP6

Variant 14-104883051-A-C is Benign according to our data. Variant chr14-104883051-A-C is described in ClinVar as Benign. ClinVar VariationId is 3058875.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=-1.84 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.647 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CEP170B	NM_001112726.3 link	c.594A>C	p.Pro198Pro	synonymous_variant	Exon 8 of 19	ENST00000414716.8	NP_001106197.1	Q9Y4F5-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CEP170B	ENST00000414716.8 link	c.594A>C	p.Pro198Pro	synonymous_variant	Exon 8 of 19	1	NM_001112726.3	ENSP00000404151.2		Q9Y4F5-2
CEP170B	ENST00000556508.5 link	c.384A>C	p.Pro128Pro	synonymous_variant	Exon 7 of 18	5		ENSP00000451249.1		Q9Y4F5-3

Frequencies

GnomAD3 genomes

AF:

0.593

AC:

89474

AN:

150994

Hom.:

27392

Cov.:

show subpopulations

Gnomad AFR

AF:

0.509

Gnomad AMI

AF:

0.632

Gnomad AMR

AF:

0.586

Gnomad ASJ

AF:

0.704

Gnomad EAS

AF:

0.219

Gnomad SAS

AF:

0.612

Gnomad FIN

AF:

0.667

Gnomad MID

AF:

0.782

Gnomad NFE

AF:

0.652

Gnomad OTH

AF:

0.626

GnomAD2 exomes

AF:

0.578

AC:

84752

AN:

146532

AF XY:

0.586

show subpopulations

Gnomad AFR exome

AF:

0.498

Gnomad AMR exome

AF:

0.527

Gnomad ASJ exome

AF:

0.703

Gnomad EAS exome

AF:

0.202

Gnomad FIN exome

AF:

0.663

Gnomad NFE exome

AF:

0.641

Gnomad OTH exome

AF:

0.610

GnomAD4 exome

AF:

0.631

AC:

869874

AN:

1377952

Hom.:

279438

Cov.:

AF XY:

0.631

AC XY:

428088

AN XY:

678104

show subpopulations

African (AFR)

AF:

0.505

AC:

15917

AN:

31516

American (AMR)

AF:

0.542

AC:

19294

AN:

35614

Ashkenazi Jewish (ASJ)

AF:

0.700

AC:

16893

AN:

24124

East Asian (EAS)

AF:

0.176

AC:

6410

AN:

36382

South Asian (SAS)

AF:

0.620

AC:

48662

AN:

78434

European-Finnish (FIN)

AF:

0.658

AC:

24454

AN:

37170

Middle Eastern (MID)

AF:

0.733

AC:

4080

AN:

5568

European-Non Finnish (NFE)

AF:

0.652

AC:

698647

AN:

1071864

Other (OTH)

AF:

0.620

AC:

35517

AN:

57280

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.486

Heterozygous variant carriers

18515

37031

55546

74062

92577

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

18594

37188

55782

74376

92970

<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:

0.592

AC:

89504

AN:

151114

Hom.:

27392

Cov.:

AF XY:

0.590

AC XY:

43557

AN XY:

73772

show subpopulations

African (AFR)

AF:

0.509

AC:

20913

AN:

41112

American (AMR)

AF:

0.585

AC:

8894

AN:

15196

Ashkenazi Jewish (ASJ)

AF:

0.704

AC:

2431

AN:

3454

East Asian (EAS)

AF:

0.219

AC:

1123

AN:

5130

South Asian (SAS)

AF:

0.613

AC:

2904

AN:

4736

European-Finnish (FIN)

AF:

0.667

AC:

7007

AN:

10498

Middle Eastern (MID)

AF:

0.772

AC:

227

AN:

294

European-Non Finnish (NFE)

AF:

0.652

AC:

44129

AN:

67698

Other (OTH)

AF:

0.623

AC:

1303

AN:

2090

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1721

3442

5162

6883

8604

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

730

1460

2190

2920

3650

<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:

0.629

Hom.:

103932

Bravo

AF:

0.582

Asia WGS

AF:

0.413

AC:

1440

AN:

3476

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

CEP170B-related disorder

Benign:1

Oct 17, 2019

PreventionGenetics, part of Exact Sciences

Significance:Benign

Review Status:no assertion criteria provided

Collection Method:clinical testing

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

0.44

(source)

DANN

Benign

0.48

PhyloP100

-1.8

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over