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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 0.385 in 151616 control chromosomes in the gnomAD Genomes database, including 11821 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.39 ( 11821 hom., cov: 30)
Exomes 𝑓: 0.42 ( 20571 hom. )

Consequence

CETP
NM_000078.3 intron

Scores

2

Clinical Significance

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

Conservation

PhyloP100: -1.65

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 (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
?
GnomAd highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.445 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
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
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
0.030
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