chr1-243156309-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 8P and 10B. PVS1BP6_ModerateBS1BS2
The ENST00000490813.5(CEP170):c.1A>G(p.Met1?) variant causes a start lost change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0314 in 1,592,400 control chromosomes in the GnomAD database, including 879 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.023 ( 45 hom., cov: 30)
Exomes 𝑓: 0.032 ( 834 hom. )
Consequence
CEP170
ENST00000490813.5 start_lost
ENST00000490813.5 start_lost
Scores
2
15
Clinical Significance
Conservation
PhyloP100: 2.33
Genes affected
CEP170 (HGNC:28920): (centrosomal protein 170) The product of this gene is a component of the centrosome, a non-membraneous organelle that functions as the major microtubule-organizing center in animal cells. During interphase, the encoded protein localizes to the sub-distal appendages of mature centrioles, which are microtubule-based structures thought to help organize centrosomes. During mitosis, the protein associates with spindle microtubules near the centrosomes. The protein interacts with and is phosphorylated by polo-like kinase 1, and functions in maintaining microtubule organization and cell morphology. The human genome contains a putative transcribed pseudogene. Several alternatively spliced transcript variants of this gene have been found, but the full-length nature of some of these variants has not been determined. [provided by RefSeq, Jul 2008]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PVS1
?
Start lost variant, no new inframe start found.
BP6
?
Variant 1-243156309-T-C is Benign according to our data. Variant chr1-243156309-T-C is described in ClinVar as [Benign]. Clinvar id is 773423.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0228 (3435/150854) while in subpopulation NFE AF= 0.0346 (2347/67796). AF 95% confidence interval is 0.0335. There are 45 homozygotes in gnomad4. There are 1591 alleles in male gnomad4 subpopulation. Median coverage is 30. This position pass quality control queck.
BS2
?
High AC in GnomAd at 3436 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CEP170 | NM_014812.3 | c.3823A>G | p.Met1275Val | missense_variant | 14/20 | ENST00000366542.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CEP170 | ENST00000366542.6 | c.3823A>G | p.Met1275Val | missense_variant | 14/20 | 5 | NM_014812.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0228 AC: 3436AN: 150736Hom.: 45 Cov.: 30
GnomAD3 genomes
?
AF:
AC:
3436
AN:
150736
Hom.:
Cov.:
30
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:
GnomAD3 exomes AF: 0.0240 AC: 4965AN: 206808Hom.: 98 AF XY: 0.0239 AC XY: 2642AN XY: 110738
GnomAD3 exomes
AF:
AC:
4965
AN:
206808
Hom.:
AF XY:
AC XY:
2642
AN XY:
110738
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.0323 AC: 46625AN: 1441546Hom.: 834 Cov.: 31 AF XY: 0.0315 AC XY: 22501AN XY: 714940
GnomAD4 exome
AF:
AC:
46625
AN:
1441546
Hom.:
Cov.:
31
AF XY:
AC XY:
22501
AN XY:
714940
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: 0.0228 AC: 3435AN: 150854Hom.: 45 Cov.: 30 AF XY: 0.0216 AC XY: 1591AN XY: 73588
GnomAD4 genome
?
AF:
AC:
3435
AN:
150854
Hom.:
Cov.:
30
AF XY:
AC XY:
1591
AN XY:
73588
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:
TwinsUK
AF:
AC:
132
ALSPAC
AF:
AC:
156
ESP6500AA
AF:
AC:
24
ESP6500EA
AF:
AC:
298
ExAC
?
AF:
AC:
2659
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Uncertain
DEOGEN2
Benign
T;.;.;.;T;.;T;T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
D
MetaRNN
Benign
T;T;T;T;T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
N;.;.;.;.;.;.;.
MutationTaster
Benign
D;D;N;N;N
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;N;N;N;N;N;N
REVEL
Benign
Sift
Benign
T;T;T;D;D;T;D;D
Sift4G
Benign
T;T;T;D;D;T;.;.
Polyphen
B;B;B;.;.;.;.;.
Vest4
ClinPred
T
GERP RS
Varity_R
gMVP
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