Genetic Variant CEP95:c.149-11T>C (chr17-64510162-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_138363.3(CEP95):c.149-11T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0554 in 1,446,602 control chromosomes in the GnomAD database, including 4,562 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 0.13 ( 2188 hom., cov: 31)

Exomes 𝑓: 0.047 ( 2374 hom. )

Consequence

CEP95
NM_138363.3 intron

Scores

Splicing: ADA: 0.00009177

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.09

Publications

7 publications found

Variant links:

Genes affected

CEP95 (HGNC:25141): (centrosomal protein 95) Located in centrosome and spindle pole. [provided by Alliance of Genome Resources, Apr 2022]

CEP95 links:

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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=-0.87).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.3 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_138363.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
CEP95	NM_138363.3	MANE Select	c.149-11T>C	intron	N/A	NP_612372.1
CEP95	NM_001316990.2		c.-238-11T>C	intron	N/A	NP_001303919.1
CEP95	NR_133644.2		n.270-11T>C	intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
CEP95	ENST00000556440.7	TSL:1 MANE Select	c.149-11T>C	intron	N/A	ENSP00000450461.2
CEP95	ENST00000553956.6	TSL:1	n.149-11T>C	intron	N/A	ENSP00000452317.2
CEP95	ENST00000581056.5	TSL:2	c.149-11T>C	intron	N/A	ENSP00000462189.1

Frequencies

GnomAD3 genomes

AF:

0.127

AC:

18875

AN:

148834

Hom.:

2178

Cov.:

show subpopulations

Gnomad AFR

AF:

0.304

Gnomad AMI

AF:

0.0356

Gnomad AMR

AF:

0.164

Gnomad ASJ

AF:

0.0453

Gnomad EAS

AF:

0.0394

Gnomad SAS

AF:

0.0359

Gnomad FIN

AF:

0.0456

Gnomad MID

AF:

0.0705

Gnomad NFE

AF:

0.0423

Gnomad OTH

AF:

0.0948

GnomAD2 exomes

AF:

0.0722

AC:

14806

AN:

205170

AF XY:

0.0638

show subpopulations

Gnomad AFR exome

AF:

0.295

Gnomad AMR exome

AF:

0.156

Gnomad ASJ exome

AF:

0.0403

Gnomad EAS exome

AF:

0.0409

Gnomad FIN exome

AF:

0.0476

Gnomad NFE exome

AF:

0.0402

Gnomad OTH exome

AF:

0.0608

GnomAD4 exome

AF:

0.0472

AC:

61284

AN:

1297664

Hom.:

2374

Cov.:

AF XY:

0.0458

AC XY:

29789

AN XY:

649790

show subpopulations

African (AFR)

AF:

0.282

AC:

8309

AN:

29422

American (AMR)

AF:

0.150

AC:

6080

AN:

40488

Ashkenazi Jewish (ASJ)

AF:

0.0402

AC:

977

AN:

24276

East Asian (EAS)

AF:

0.0396

AC:

1530

AN:

38670

South Asian (SAS)

AF:

0.0329

AC:

2639

AN:

80216

European-Finnish (FIN)

AF:

0.0479

AC:

2464

AN:

51394

Middle Eastern (MID)

AF:

0.0465

AC:

257

AN:

5526

European-Non Finnish (NFE)

AF:

0.0370

AC:

36004

AN:

972866

Other (OTH)

AF:

0.0552

AC:

3024

AN:

54806

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.465

Heterozygous variant carriers

2321

4643

6964

9286

11607

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1398

2796

4194

5592

6990

<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:

0.127

AC:

18921

AN:

148938

Hom.:

2188

Cov.:

AF XY:

0.127

AC XY:

9199

AN XY:

72710

show subpopulations

African (AFR)

AF:

0.304

AC:

12412

AN:

40832

American (AMR)

AF:

0.164

AC:

2467

AN:

15052

Ashkenazi Jewish (ASJ)

AF:

0.0453

AC:

155

AN:

3424

East Asian (EAS)

AF:

0.0394

AC:

203

AN:

5158

South Asian (SAS)

AF:

0.0362

AC:

171

AN:

4730

European-Finnish (FIN)

AF:

0.0456

AC:

466

AN:

10230

Middle Eastern (MID)

AF:

0.0764

AC:

AN:

288

European-Non Finnish (NFE)

AF:

0.0423

AC:

2801

AN:

66278

Other (OTH)

AF:

0.0938

AC:

192

AN:

2048

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.487

Heterozygous variant carriers

676

1352

2029

2705

3381

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

180

360

540

720

900

<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:

0.0979

Hom.:

419

Bravo

AF:

0.141

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.82

(source)

DANN

Benign

0.46

PhyloP100

-1.1

PromoterAI

0.0052

Neutral

(source)

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.000092

dbscSNV1_RF

Benign

0.0020

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over