18-13001489-A-G
Position:
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_032142.4(CEP192):āc.197A>Gā(p.Glu66Gly) variant causes a missense change. The variant allele was found at a frequency of 0.000433 in 1,549,698 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: š 0.00043 ( 0 hom., cov: 33)
Exomes š: 0.00043 ( 0 hom. )
Consequence
CEP192
NM_032142.4 missense
NM_032142.4 missense
Scores
1
2
15
Clinical Significance
Conservation
PhyloP100: 4.33
Genes affected
CEP192 (HGNC:25515): (centrosomal protein 192) Enables phosphatase binding activity. Involved in centrosome-templated microtubule nucleation; mitotic spindle assembly; and protein localization to centrosome. Located in centriole; centrosome; and cytosol. [provided by Alliance of Genome Resources, Apr 2022]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.03146863).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CEP192 | NM_032142.4 | c.197A>G | p.Glu66Gly | missense_variant | 3/45 | ENST00000506447.5 | NP_115518.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CEP192 | ENST00000506447.5 | c.197A>G | p.Glu66Gly | missense_variant | 3/45 | 5 | NM_032142.4 | ENSP00000427550 | P1 | |
CEP192 | ENST00000589596.5 | c.197A>G | p.Glu66Gly | missense_variant | 3/18 | 2 | ENSP00000466258 | |||
CEP192 | ENST00000325971.12 | c.-1019A>G | 5_prime_UTR_variant | 3/44 | 5 | ENSP00000317156 | ||||
CEP192 | ENST00000507064.2 | c.*159A>G | 3_prime_UTR_variant, NMD_transcript_variant | 4/5 | 3 | ENSP00000476907 |
Frequencies
GnomAD3 genomes AF: 0.000434 AC: 66AN: 152172Hom.: 0 Cov.: 33
GnomAD3 genomes
AF:
AC:
66
AN:
152172
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:
GnomAD3 exomes AF: 0.000359 AC: 55AN: 153404Hom.: 0 AF XY: 0.000246 AC XY: 20AN XY: 81404
GnomAD3 exomes
AF:
AC:
55
AN:
153404
Hom.:
AF XY:
AC XY:
20
AN XY:
81404
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: 0.000433 AC: 605AN: 1397408Hom.: 0 Cov.: 28 AF XY: 0.000418 AC XY: 288AN XY: 689360
GnomAD4 exome
AF:
AC:
605
AN:
1397408
Hom.:
Cov.:
28
AF XY:
AC XY:
288
AN XY:
689360
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: 0.000433 AC: 66AN: 152290Hom.: 0 Cov.: 33 AF XY: 0.000322 AC XY: 24AN XY: 74462
GnomAD4 genome
AF:
AC:
66
AN:
152290
Hom.:
Cov.:
33
AF XY:
AC XY:
24
AN XY:
74462
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:
2
ALSPAC
AF:
AC:
0
ExAC
AF:
AC:
4
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 08, 2022 | The c.197A>G (p.E66G) alteration is located in exon 3 (coding exon 2) of the CEP192 gene. This alteration results from a A to G substitution at nucleotide position 197, causing the glutamic acid (E) at amino acid position 66 to be replaced by a glycine (G). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T;T
M_CAP
Benign
T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationTaster
Benign
N;N
PrimateAI
Benign
T
PROVEAN
Benign
.;N
REVEL
Benign
Sift
Uncertain
.;D
Sift4G
Pathogenic
D;D
Vest4
0.20
MVP
MPC
0.14
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