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GeneBe

rs5882

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_000078.3(CETP):c.1264G>A(p.Val422Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.59 in 151834 control chromosomes in the gnomAD Genomes database, including 27562 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.59 ( 27562 hom., cov: 31)
Exomes 𝑓: 0.62 ( 48877 hom. )

Consequence

CETP
NM_000078.3 missense

Scores

18

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:6O:1

Conservation

PhyloP100: -2.36

Links

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4
?
Computational evidence support a benign effect (MetaRNN=3.5843727E-6).
BP6
?
Variant 16-56982180-G-A is Benign according to our data. Variant chr16-56982180-G-A is described in ClinVar as [Benign]. Clinvar id is 17525. Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-56982180-G-A is described in Lovd as [Benign].
BA1
?
GnomAd highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.678 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CETPNM_000078.3 linkuse as main transcriptc.1264G>A p.Val422Ile missense_variant 14/16 ENST00000200676.8
CETPNM_001286085.2 linkuse as main transcriptc.1084G>A p.Val362Ile missense_variant 13/15

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CETPENST00000200676.8 linkuse as main transcriptc.1264G>A p.Val422Ile missense_variant 14/161 NM_000078.3 P1P11597-1
CETPENST00000379780.6 linkuse as main transcriptc.1084G>A p.Val362Ile missense_variant 13/151 P11597-2
CETPENST00000566128.1 linkuse as main transcriptc.1069G>A p.Val357Ile missense_variant 14/165
CETPENST00000650358.1 linkuse as main transcriptn.1662G>A non_coding_transcript_exon_variant 4/5

Frequencies

GnomAD3 genomes
AF:
0.590
AC:
89567
AN:
151834
Hom.:
27562
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.425
Gnomad AMI
AF:
0.460
Gnomad AMR
AF:
0.627
Gnomad ASJ
AF:
0.585
Gnomad EAS
AF:
0.555
Gnomad SAS
AF:
0.563
Gnomad FIN
AF:
0.622
Gnomad MID
AF:
0.576
Gnomad NFE
AF:
0.683
Gnomad OTH
AF:
0.620
GnomAD3 exomes
AF:
0.619
AC:
155510
AN:
251372
Hom.:
48877
AF XY:
0.624
AC XY:
84847
AN XY:
135866
show subpopulations
Gnomad AFR exome
AF:
0.418
Gnomad AMR exome
AF:
0.586
Gnomad ASJ exome
AF:
0.592
Gnomad EAS exome
AF:
0.554
Gnomad SAS exome
AF:
0.567
Gnomad FIN exome
AF:
0.621
Gnomad NFE exome
AF:
0.684
Gnomad OTH exome
AF:
0.617
GnomAD4 exome
AF:
0.658
AC:
961601
AN:
1461446
Hom.:
319314
AF XY:
0.656
AC XY:
477060
AN XY:
727052
show subpopulations
Gnomad4 AFR exome
AF:
0.411
Gnomad4 AMR exome
AF:
0.592
Gnomad4 ASJ exome
AF:
0.589
Gnomad4 EAS exome
AF:
0.520
Gnomad4 SAS exome
AF:
0.569
Gnomad4 FIN exome
AF:
0.617
Gnomad4 NFE exome
AF:
0.685
Gnomad4 OTH exome
AF:
0.638
Alfa
AF:
0.657
Hom.:
81813
Bravo
AF:
0.580
TwinsUK
AF:
0.687
AC:
2549
ALSPAC
AF:
0.676
AC:
2605
ESP6500AA
AF:
0.415
AC:
1823
ESP6500EA
AF:
0.681
AC:
5860
ExAC
AF:
0.616
AC:
74827
Asia WGS
AF:
0.533
AC:
1857
AN:
3478
EpiCase
AF:
0.682
EpiControl
AF:
0.672

ClinVar

Significance: Benign
Submissions summary: Benign:6Other:1
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:2
Benign, criteria provided, single submitterclinical testingGeneDxAug 30, 2018This variant is associated with the following publications: (PMID: 10092998, 23977315, 25260850, 22464147, 21767357, 20068209, 14559957, 19242900, 23274582, 22122979) -
Benign, criteria provided, single submitterclinical testingInvitaeNov 04, 2022- -
Hyperalphalipoproteinemia 1 Benign:2
Benign, no assertion criteria providedclinical testingDiagnostic Laboratory, Department of Genetics, University Medical Center Groningen-- -
Benign, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaApr 27, 2017This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign. -
not specified Benign:1
Benign, no assertion criteria providedclinical testingClinical Genetics, Academic Medical Center-- -
Coronary artery disorder Benign:1
Benign, criteria provided, single submitterclinical testingRasad Genetic Department, Rasad Pathobiology and Genetic LaboratoryMay 12, 2022- -
High density lipoprotein cholesterol level quantitative trait locus 10 Other:1
association, no assertion criteria providedliterature onlyOMIMJan 13, 2010- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.068
BayesDel_addAF
Benign
-0.88
T
BayesDel_noAF
Benign
-0.89
Cadd
Benign
0.0010
Dann
Benign
0.24
DEOGEN2
Benign
0.070
T;.;T
Eigen
Benign
-1.7
Eigen_PC
Benign
-1.8
FATHMM_MKL
Benign
0.0043
N
LIST_S2
Benign
0.50
T;T;T
MetaRNN
Benign
0.0000036
T;T;T
MetaSVM
Benign
-0.99
T
MutationAssessor
Benign
-0.57
N;.;.
MutationTaster
Benign
1.0
P;P;P
PrimateAI
Benign
0.29
T
PROVEAN
Benign
0.52
N;N;N
REVEL
Benign
0.013
Sift
Benign
1.0
T;T;T
Sift4G
Benign
1.0
T;T;T
Polyphen
0.0010
B;B;.
Vest4
0.028
MPC
0.11
ClinPred
0.0086
T
GERP RS
-6.7
Varity_R
0.017
gMVP
0.088

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
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: rs5882; hg19: chr16-57016092; COSMIC: COSV52364598; API