chr5-123346272-A-T
Variant names:
Variant summary
Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001375405.1(CEP120):c.*247T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00288 in 383,468 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0061 ( 8 hom., cov: 33)
Exomes 𝑓: 0.00074 ( 1 hom. )
Consequence
CEP120
NM_001375405.1 3_prime_UTR
NM_001375405.1 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.555
Publications
1 publications found
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):
- ciliopathyInheritance: AR Classification: DEFINITIVE Submitted by: G2P
- Joubert syndrome 31Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
- short-rib thoracic dysplasia 13 with or without polydactylyInheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
- Jeune syndromeInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
- Joubert syndromeInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
- Joubert syndrome with ocular defectInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
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=-0.52).
BP6
Variant 5-123346272-A-T is Benign according to our data. Variant chr5-123346272-A-T is described in ClinVar as [Likely_benign]. Clinvar id is 1213615.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.00614 (935/152326) while in subpopulation AFR AF = 0.0209 (871/41576). AF 95% confidence interval is 0.0198. There are 8 homozygotes in GnomAd4. There are 443 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
BS2
High Homozygotes in GnomAd4 at 8 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CEP120 | NM_001375405.1 | c.*247T>A | 3_prime_UTR_variant | Exon 20 of 20 | ENST00000306467.10 | NP_001362334.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00613 AC: 933AN: 152208Hom.: 7 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
933
AN:
152208
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.000735 AC: 170AN: 231142Hom.: 1 Cov.: 0 AF XY: 0.000609 AC XY: 73AN XY: 119918 show subpopulations
GnomAD4 exome
AF:
AC:
170
AN:
231142
Hom.:
Cov.:
0
AF XY:
AC XY:
73
AN XY:
119918
show subpopulations
African (AFR)
AF:
AC:
120
AN:
6412
American (AMR)
AF:
AC:
16
AN:
8334
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
8164
East Asian (EAS)
AF:
AC:
0
AN:
17458
South Asian (SAS)
AF:
AC:
0
AN:
13398
European-Finnish (FIN)
AF:
AC:
0
AN:
14434
Middle Eastern (MID)
AF:
AC:
1
AN:
1158
European-Non Finnish (NFE)
AF:
AC:
5
AN:
147260
Other (OTH)
AF:
AC:
28
AN:
14524
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.499
Heterozygous variant carriers
0
9
19
28
38
47
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome AF: 0.00614 AC: 935AN: 152326Hom.: 8 Cov.: 33 AF XY: 0.00595 AC XY: 443AN XY: 74476 show subpopulations
GnomAD4 genome
AF:
AC:
935
AN:
152326
Hom.:
Cov.:
33
AF XY:
AC XY:
443
AN XY:
74476
show subpopulations
African (AFR)
AF:
AC:
871
AN:
41576
American (AMR)
AF:
AC:
53
AN:
15298
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3468
East Asian (EAS)
AF:
AC:
0
AN:
5190
South Asian (SAS)
AF:
AC:
0
AN:
4830
European-Finnish (FIN)
AF:
AC:
0
AN:
10626
Middle Eastern (MID)
AF:
AC:
0
AN:
294
European-Non Finnish (NFE)
AF:
AC:
1
AN:
68022
Other (OTH)
AF:
AC:
10
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.498
Heterozygous variant carriers
0
45
89
134
178
223
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
10
AN:
3468
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Oct 05, 2018
GeneDx
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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