Genetic Variant CEP120:p.Asp942Asp (chr5-123346654-A-G) – ACMG Classification: Benign (-21 pts)

Variant summary

Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001375405.1(CEP120):c.2826T>C(p.Asp942Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.703 in 1,613,262 control chromosomes in the GnomAD database, including 399,949 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.72 ( 38994 hom., cov: 31)

Exomes 𝑓: 0.70 ( 360955 hom. )

Consequence

CEP120
NM_001375405.1 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: 0.325

Publications

20 publications found

Variant links:

Genes affected

CEP120 (HGNC:26690): (centrosomal protein 120) This gene encodes a protein that functions in the microtubule-dependent coupling of the nucleus and the centrosome. A similar protein in mouse plays a role in both interkinetic nuclear migration, which is a characteristic pattern of nuclear movement in neural progenitors, and in neural progenitor self-renewal. Mutations in this gene are predicted to result in neurogenic defects. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2009]

CEP120 Gene-Disease associations (from GenCC):

ciliopathy
Inheritance: AR Classification: DEFINITIVE Submitted by: G2P
Joubert syndrome 31
Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
short-rib thoracic dysplasia 13 with or without polydactyly
Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
Jeune syndrome
Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
Joubert syndrome
Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
Joubert syndrome with ocular defect
Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

CEP120 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.53).

BP6

Variant 5-123346654-A-G is Benign according to our data. Variant chr5-123346654-A-G is described in ClinVar as Benign. ClinVar VariationId is 1167916.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.325 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.743 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001375405.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
CEP120	NM_001375405.1	MANE Select	c.2826T>C	p.Asp942Asp	synonymous	Exon 20 of 20	NP_001362334.1	Q8N960-1
CEP120	NM_153223.4		c.2826T>C	p.Asp942Asp	synonymous	Exon 21 of 21	NP_694955.2	Q8N960-1
CEP120	NM_001166226.2		c.2748T>C	p.Asp916Asp	synonymous	Exon 20 of 20	NP_001159698.1	Q8N960-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
CEP120	ENST00000306467.10	TSL:5 MANE Select	c.2826T>C	p.Asp942Asp	synonymous	Exon 20 of 20	ENSP00000303058.6	Q8N960-1
CEP120	ENST00000508138.5	TSL:1	n.*2398T>C		non_coding_transcript_exon	Exon 23 of 23	ENSP00000422234.1	D6R8Z4
CEP120	ENST00000513565.6	TSL:1	n.*2230T>C		non_coding_transcript_exon	Exon 21 of 21	ENSP00000422089.2	Q8N960-3

Frequencies

GnomAD3 genomes

AF:

0.715

AC:

108573

AN:

151868

Hom.:

38947

Cov.:

show subpopulations

Gnomad AFR

AF:

0.749

Gnomad AMI

AF:

0.727

Gnomad AMR

AF:

0.712

Gnomad ASJ

AF:

0.736

Gnomad EAS

AF:

0.574

Gnomad SAS

AF:

0.665

Gnomad FIN

AF:

0.708

Gnomad MID

AF:

0.734

Gnomad NFE

AF:

0.708

Gnomad OTH

AF:

0.746

GnomAD2 exomes

AF:

0.690

AC:

173191

AN:

250918

AF XY:

0.692

show subpopulations

Gnomad AFR exome

AF:

0.754

Gnomad AMR exome

AF:

0.634

Gnomad ASJ exome

AF:

0.734

Gnomad EAS exome

AF:

0.575

Gnomad FIN exome

AF:

0.711

Gnomad NFE exome

AF:

0.714

Gnomad OTH exome

AF:

0.706

GnomAD4 exome

AF:

0.702

AC:

1025252

AN:

1461276

Hom.:

360955

Cov.:

AF XY:

0.700

AC XY:

509193

AN XY:

726908

show subpopulations

African (AFR)

AF:

0.751

AC:

25144

AN:

33466

American (AMR)

AF:

0.646

AC:

28825

AN:

44588

Ashkenazi Jewish (ASJ)

AF:

0.730

AC:

19060

AN:

26126

East Asian (EAS)

AF:

0.551

AC:

21881

AN:

39678

South Asian (SAS)

AF:

0.668

AC:

57559

AN:

86154

European-Finnish (FIN)

AF:

0.711

AC:

37969

AN:

53372

Middle Eastern (MID)

AF:

0.746

AC:

4299

AN:

5762

European-Non Finnish (NFE)

AF:

0.709

AC:

787992

AN:

1111762

Other (OTH)

AF:

0.704

AC:

42523

AN:

60368

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.474

Heterozygous variant carriers

16405

32810

49215

65620

82025

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

19776

39552

59328

79104

98880

<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:

0.715

AC:

108678

AN:

151986

Hom.:

38994

Cov.:

AF XY:

0.712

AC XY:

52857

AN XY:

74260

show subpopulations

African (AFR)

AF:

0.750

AC:

31085

AN:

41460

American (AMR)

AF:

0.712

AC:

10862

AN:

15264

Ashkenazi Jewish (ASJ)

AF:

0.736

AC:

2555

AN:

3472

East Asian (EAS)

AF:

0.574

AC:

2954

AN:

5150

South Asian (SAS)

AF:

0.665

AC:

3204

AN:

4816

European-Finnish (FIN)

AF:

0.708

AC:

7482

AN:

10562

Middle Eastern (MID)

AF:

0.735

AC:

216

AN:

294

European-Non Finnish (NFE)

AF:

0.708

AC:

48081

AN:

67948

Other (OTH)

AF:

0.747

AC:

1577

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1589

3178

4766

6355

7944

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

832

1664

2496

3328

4160

<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:

0.714

Hom.:

118374

Bravo

AF:

0.719

Asia WGS

AF:

0.663

AC:

2304

AN:

3478

EpiCase

AF:

0.725

EpiControl

AF:

0.721

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

Short-rib thoracic dysplasia 13 with or without polydactyly (2)

Joubert syndrome 31 (1)

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.53

CADD

Benign

4.3

(source)

DANN

Benign

0.49

PhyloP100

0.33

Mutation Taster

=95/5

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

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