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rs708272

Variant summary

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

The NM_000078.3(CETP):c.118+279G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.414 in 665,408 control chromosomes in the GnomAD database, including 58,748 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.39 ( 11832 hom., cov: 30)
Exomes 𝑓: 0.42 ( 46916 hom. )

Consequence

CETP
NM_000078.3 intron

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -1.65
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 Benign. Variant got -20 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.98).
BP6
Variant 16-56962376-G-A is Benign according to our data. Variant chr16-56962376-G-A is described in ClinVar as [Benign]. Clinvar id is 1239762.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-56962376-G-A is described in Lovd as [Benign].
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.446 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CETPNM_000078.3 linkuse as main transcriptc.118+279G>A intron_variant ENST00000200676.8
CETPNM_001286085.2 linkuse as main transcriptc.118+279G>A intron_variant
CETPXM_006721124.4 linkuse as main transcriptc.118+279G>A intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CETPENST00000200676.8 linkuse as main transcriptc.118+279G>A intron_variant 1 NM_000078.3 P1P11597-1
CETPENST00000379780.6 linkuse as main transcriptc.118+279G>A intron_variant 1 P11597-2
CETPENST00000566128.1 linkuse as main transcriptc.-78+80G>A intron_variant 5
CETPENST00000569082.1 linkuse as main transcriptn.116+279G>A intron_variant, non_coding_transcript_variant 5

Frequencies

GnomAD3 genomes
AF:
0.385
AC:
58415
AN:
151616
Hom.:
11821
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.264
Gnomad AMI
AF:
0.525
Gnomad AMR
AF:
0.419
Gnomad ASJ
AF:
0.384
Gnomad EAS
AF:
0.375
Gnomad SAS
AF:
0.461
Gnomad FIN
AF:
0.452
Gnomad MID
AF:
0.402
Gnomad NFE
AF:
0.434
Gnomad OTH
AF:
0.384
GnomAD3 exomes
AF:
0.424
AC:
96025
AN:
226300
Hom.:
20571
AF XY:
0.428
AC XY:
53503
AN XY:
124984
show subpopulations
Gnomad AFR exome
AF:
0.262
Gnomad AMR exome
AF:
0.476
Gnomad ASJ exome
AF:
0.378
Gnomad EAS exome
AF:
0.392
Gnomad SAS exome
AF:
0.465
Gnomad FIN exome
AF:
0.437
Gnomad NFE exome
AF:
0.426
Gnomad OTH exome
AF:
0.426
GnomAD4 exome
AF:
0.423
AC:
217317
AN:
513672
Hom.:
46916
Cov.:
0
AF XY:
0.427
AC XY:
121515
AN XY:
284554
show subpopulations
Gnomad4 AFR exome
AF:
0.253
Gnomad4 AMR exome
AF:
0.469
Gnomad4 ASJ exome
AF:
0.373
Gnomad4 EAS exome
AF:
0.380
Gnomad4 SAS exome
AF:
0.471
Gnomad4 FIN exome
AF:
0.439
Gnomad4 NFE exome
AF:
0.421
Gnomad4 OTH exome
AF:
0.410
GnomAD4 genome
AF:
0.385
AC:
58469
AN:
151736
Hom.:
11832
Cov.:
30
AF XY:
0.390
AC XY:
28940
AN XY:
74114
show subpopulations
Gnomad4 AFR
AF:
0.265
Gnomad4 AMR
AF:
0.420
Gnomad4 ASJ
AF:
0.384
Gnomad4 EAS
AF:
0.375
Gnomad4 SAS
AF:
0.462
Gnomad4 FIN
AF:
0.452
Gnomad4 NFE
AF:
0.434
Gnomad4 OTH
AF:
0.382
Alfa
AF:
0.426
Hom.:
15714
Bravo
AF:
0.376
Asia WGS
AF:
0.407
AC:
1417
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

Coronary artery disorder Benign:1
Benign, criteria provided, single submitterclinical testingRasad Genetic Department, Rasad Pathobiology and Genetic LaboratoryMay 12, 2022- -
not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxAug 30, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.98
Cadd
Benign
0.049
Dann
Benign
0.39

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
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: rs708272; hg19: chr16-56996288; COSMIC: COSV52361236; API