rs115701891

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The NM_025009.5(CEP135):​c.1675G>A​(p.Ala559Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00192 in 1,597,440 control chromosomes in the GnomAD database, including 56 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.011 ( 29 hom., cov: 32)
Exomes 𝑓: 0.0010 ( 27 hom. )

Consequence

CEP135
NM_025009.5 missense

Scores

18

Clinical Significance

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

Conservation

PhyloP100: -0.577
Variant links:
Genes affected
CEP135 (HGNC:29086): (centrosomal protein 135) This gene encodes a centrosomal protein, which acts as a scaffolding protein during early centriole biogenesis, and is also required for centriole-centriole cohesion during interphase. Mutations in this gene are associated with autosomal recessive primary microcephaly-8. [provided by RefSeq, Jun 2012]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.0023153126).
BP6
Variant 4-55981275-G-A is Benign according to our data. Variant chr4-55981275-G-A is described in ClinVar as [Benign]. Clinvar id is 128694.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0106 (1605/152090) while in subpopulation AFR AF= 0.0371 (1537/41476). AF 95% confidence interval is 0.0355. There are 29 homozygotes in gnomad4. There are 764 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 29 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CEP135NM_025009.5 linkuse as main transcriptc.1675G>A p.Ala559Thr missense_variant 13/26 ENST00000257287.5 NP_079285.2 Q66GS9-1
CEP135XM_006714055.4 linkuse as main transcriptc.1642G>A p.Ala548Thr missense_variant 13/26 XP_006714118.1
CEP135XM_005265788.5 linkuse as main transcriptc.604G>A p.Ala202Thr missense_variant 6/19 XP_005265845.1
CEP135XM_011534412.2 linkuse as main transcriptc.145G>A p.Ala49Thr missense_variant 3/16 XP_011532714.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CEP135ENST00000257287.5 linkuse as main transcriptc.1675G>A p.Ala559Thr missense_variant 13/261 NM_025009.5 ENSP00000257287.3 Q66GS9-1
CEP135ENST00000506202.1 linkuse as main transcriptn.1625G>A non_coding_transcript_exon_variant 6/191

Frequencies

GnomAD3 genomes
AF:
0.0106
AC:
1605
AN:
151972
Hom.:
29
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0372
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00315
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00316
Gnomad NFE
AF:
0.0000735
Gnomad OTH
AF:
0.00669
GnomAD3 exomes
AF:
0.00269
AC:
634
AN:
235322
Hom.:
11
AF XY:
0.00198
AC XY:
252
AN XY:
127456
show subpopulations
Gnomad AFR exome
AF:
0.0394
Gnomad AMR exome
AF:
0.00102
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000643
Gnomad OTH exome
AF:
0.000894
GnomAD4 exome
AF:
0.00102
AC:
1470
AN:
1445350
Hom.:
27
Cov.:
30
AF XY:
0.000892
AC XY:
641
AN XY:
718268
show subpopulations
Gnomad4 AFR exome
AF:
0.0394
Gnomad4 AMR exome
AF:
0.00108
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000122
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000181
Gnomad4 OTH exome
AF:
0.00209
GnomAD4 genome
AF:
0.0106
AC:
1605
AN:
152090
Hom.:
29
Cov.:
32
AF XY:
0.0103
AC XY:
764
AN XY:
74336
show subpopulations
Gnomad4 AFR
AF:
0.0371
Gnomad4 AMR
AF:
0.00314
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000735
Gnomad4 OTH
AF:
0.00662
Alfa
AF:
0.00195
Hom.:
4
Bravo
AF:
0.0119
ESP6500AA
AF:
0.0399
AC:
176
ESP6500EA
AF:
0.000116
AC:
1
ExAC
AF:
0.00360
AC:
437
Asia WGS
AF:
0.00115
AC:
4
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:3
Benign, criteria provided, single submitterclinical testingGeneDxMar 22, 2019- -
Benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -
Benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpJan 22, 2024- -
not specified Benign:1
Benign, criteria provided, single submitterclinical testingGenetic Services Laboratory, University of ChicagoApr 03, 2013- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.063
BayesDel_addAF
Benign
-0.75
T
BayesDel_noAF
Benign
-0.82
CADD
Benign
6.5
DANN
Benign
0.16
DEOGEN2
Benign
0.0037
T
Eigen
Benign
-1.3
Eigen_PC
Benign
-1.3
FATHMM_MKL
Benign
0.027
N
LIST_S2
Benign
0.54
T
MetaRNN
Benign
0.0023
T
MetaSVM
Benign
-1.1
T
MutationAssessor
Benign
-0.34
N
PrimateAI
Benign
0.23
T
PROVEAN
Benign
-0.23
N
REVEL
Benign
0.013
Sift
Benign
0.69
T
Sift4G
Benign
0.33
T
Polyphen
0.16
B
Vest4
0.065
MVP
0.20
MPC
0.057
ClinPred
0.0034
T
GERP RS
0.56
Varity_R
0.028
gMVP
0.051

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs115701891; hg19: chr4-56847441; API