chr4-55952526-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_025009.5(CEP135):c.113+283C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00455 in 248,166 control chromosomes in the GnomAD database, including 14 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0055 ( 12 hom., cov: 33)
Exomes 𝑓: 0.0030 ( 2 hom. )
Consequence
CEP135
NM_025009.5 intron
NM_025009.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.750
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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BP6
?
Variant 4-55952526-C-T is Benign according to our data. Variant chr4-55952526-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1198071.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00554 (844/152264) while in subpopulation NFE AF= 0.00384 (261/68020). AF 95% confidence interval is 0.00345. There are 12 homozygotes in gnomad4. There are 552 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 12 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CEP135 | NM_025009.5 | c.113+283C>T | intron_variant | ENST00000257287.5 | |||
LOC124900705 | XR_007058124.1 | n.198-55G>A | intron_variant, non_coding_transcript_variant | ||||
CEP135 | XM_006714055.4 | c.113+283C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CEP135 | ENST00000257287.5 | c.113+283C>T | intron_variant | 1 | NM_025009.5 | P1 | |||
CEP135 | ENST00000422247.6 | c.113+283C>T | intron_variant | 2 | |||||
CEP135 | ENST00000506809.1 | n.556C>T | non_coding_transcript_exon_variant | 2/2 | 3 | ||||
CEP135 | ENST00000706800.1 | n.286+283C>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.00555 AC: 844AN: 152146Hom.: 12 Cov.: 33
GnomAD3 genomes
?
AF:
AC:
844
AN:
152146
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: 0.00298 AC: 286AN: 95902Hom.: 2 Cov.: 0 AF XY: 0.00316 AC XY: 155AN XY: 49102
GnomAD4 exome
AF:
AC:
286
AN:
95902
Hom.:
Cov.:
0
AF XY:
AC XY:
155
AN XY:
49102
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.00554 AC: 844AN: 152264Hom.: 12 Cov.: 33 AF XY: 0.00741 AC XY: 552AN XY: 74458
GnomAD4 genome
?
AF:
AC:
844
AN:
152264
Hom.:
Cov.:
33
AF XY:
AC XY:
552
AN XY:
74458
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
2
AN:
3478
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Sep 11, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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