16-56962068-G-A

Variant summary

Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BP6

The NM_000078.3(CETP):​c.89G>A​(p.Cys30Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000397 in 1,613,972 control chromosomes in the GnomAD database, including 1 homozygotes. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

Frequency

Genomes: 𝑓 0.000072 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000036 ( 1 hom. )

Consequence

CETP
NM_000078.3 missense

Scores

2
7
10

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:1B:1

Conservation

PhyloP100: 2.39
Variant links:
Genes affected
CETP (HGNC:1869): (cholesteryl ester transfer protein) The protein encoded by this gene is found in plasma, where it is involved in the transfer of cholesteryl ester from high density lipoprotein (HDL) to other lipoproteins. Defects in this gene are a cause of hyperalphalipoproteinemia 1 (HALP1). Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2013]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -1 ACMG points.

BP6
Variant 16-56962068-G-A is Benign according to our data. Variant chr16-56962068-G-A is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 1314022.We mark this variant Likely_benign, oryginal submissions are: {Likely_benign=1, Uncertain_significance=1}.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CETPNM_000078.3 linkuse as main transcriptc.89G>A p.Cys30Tyr missense_variant 1/16 ENST00000200676.8 NP_000069.2
CETPNM_001286085.2 linkuse as main transcriptc.89G>A p.Cys30Tyr missense_variant 1/15 NP_001273014.1
CETPXM_006721124.4 linkuse as main transcriptc.89G>A p.Cys30Tyr missense_variant 1/9 XP_006721187.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CETPENST00000200676.8 linkuse as main transcriptc.89G>A p.Cys30Tyr missense_variant 1/161 NM_000078.3 ENSP00000200676 P1P11597-1
CETPENST00000379780.6 linkuse as main transcriptc.89G>A p.Cys30Tyr missense_variant 1/151 ENSP00000369106 P11597-2
CETPENST00000569082.1 linkuse as main transcriptn.87G>A non_coding_transcript_exon_variant 1/95
CETPENST00000566128.1 linkuse as main transcript upstream_gene_variant 5 ENSP00000456276

Frequencies

GnomAD3 genomes
AF:
0.0000723
AC:
11
AN:
152230
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000720
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000139
AC:
35
AN:
251032
Hom.:
0
AF XY:
0.000103
AC XY:
14
AN XY:
135720
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.000983
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:
0.00
Gnomad OTH exome
AF:
0.000163
GnomAD4 exome
AF:
0.0000363
AC:
53
AN:
1461742
Hom.:
1
Cov.:
31
AF XY:
0.0000248
AC XY:
18
AN XY:
727178
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00119
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.0000723
AC:
11
AN:
152230
Hom.:
0
Cov.:
32
AF XY:
0.0000807
AC XY:
6
AN XY:
74384
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.000720
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00
Bravo
AF:
0.0000793
ExAC
AF:
0.0000494
AC:
6

ClinVar

Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:1Benign:1
Revision: criteria provided, conflicting classifications
LINK: link

Submissions by phenotype

not provided Uncertain:1Benign:1
Uncertain significance, criteria provided, single submitterclinical testingGeneDxJan 19, 2021Has not been previously published as pathogenic or benign to our knowledge; In silico analysis supports that this missense variant has a deleterious effect on protein structure/function -
Likely benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpNov 01, 2023- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.79
BayesDel_addAF
Benign
-0.40
T
BayesDel_noAF
Benign
-0.40
CADD
Benign
23
DANN
Uncertain
0.99
DEOGEN2
Uncertain
0.69
D;.
Eigen
Benign
0.061
Eigen_PC
Benign
-0.023
FATHMM_MKL
Benign
0.56
D
LIST_S2
Benign
0.84
T;D
M_CAP
Benign
0.047
D
MetaRNN
Uncertain
0.44
T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Uncertain
2.1
M;M
MutationTaster
Benign
0.52
D;D
PrimateAI
Uncertain
0.55
T
PROVEAN
Pathogenic
-4.8
D;D
REVEL
Benign
0.20
Sift
Uncertain
0.013
D;D
Sift4G
Uncertain
0.052
T;T
Polyphen
1.0
D;D
Vest4
0.59
MutPred
0.63
Gain of catalytic residue at C30 (P = 0.098);Gain of catalytic residue at C30 (P = 0.098);
MVP
0.36
MPC
0.71
ClinPred
0.55
D
GERP RS
3.1
Varity_R
0.66
gMVP
0.90

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: rs771585518; hg19: chr16-56995980; API