Variant rs289714 details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000200676.8(CETP):c.930+29G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.795 in 1,612,824 control chromosomes in the GnomAD database, including 515,566 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.71 ( 39930 hom., cov: 31)

Exomes 𝑓: 0.80 ( 475636 hom. )

Consequence

CETP
ENST00000200676.8 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.996

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]

CETP links:

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=-0.91).

BP6

Variant 16-56973539-G-A is Benign according to our data. Variant chr16-56973539-G-A is described in ClinVar as [Benign]. Clinvar id is 1181918.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-56973539-G-A is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.815 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CETP	NM_000078.3 linkuse as main transcript	c.930+29G>A		intron_variant		ENST00000200676.8	NP_000069.2
CETP	NM_001286085.2 linkuse as main transcript	c.750+1456G>A		intron_variant			NP_001273014.1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	Appris	UniProt
CETP	ENST00000200676.8 linkuse as main transcript	c.930+29G>A	intron_variant	1	NM_000078.3	ENSP00000200676	P1	P11597-1
CETP	ENST00000379780.6 linkuse as main transcript	c.750+1456G>A	intron_variant	1		ENSP00000369106		P11597-2
CETP	ENST00000566128.1 linkuse as main transcript	c.735+29G>A	intron_variant	5		ENSP00000456276

Frequencies

GnomAD3 genomes

AF:

0.706

AC:

107323

AN:

152000

Hom.:

39919

Cov.:

show subpopulations

Gnomad AFR

AF:

0.463

Gnomad AMI

AF:

0.888

Gnomad AMR

AF:

0.679

Gnomad ASJ

AF:

0.839

Gnomad EAS

AF:

0.734

Gnomad SAS

AF:

0.767

Gnomad FIN

AF:

0.851

Gnomad MID

AF:

0.771

Gnomad NFE

AF:

0.821

Gnomad OTH

AF:

0.718

GnomAD3 exomes

AF:

0.763

AC:

190435

AN:

249608

Hom.:

73909

AF XY:

0.772

AC XY:

104161

AN XY:

134958

show subpopulations

Gnomad AFR exome

AF:

0.457

Gnomad AMR exome

AF:

0.661

Gnomad ASJ exome

AF:

0.841

Gnomad EAS exome

AF:

0.721

Gnomad SAS exome

AF:

0.757

Gnomad FIN exome

AF:

0.842

Gnomad NFE exome

AF:

0.822

Gnomad OTH exome

AF:

0.798

GnomAD4 exome

AF:

0.804

AC:

1174662

AN:

1460704

Hom.:

475636

Cov.:

AF XY:

0.805

AC XY:

584706

AN XY:

726658

show subpopulations

Gnomad4 AFR exome

AF:

0.457

Gnomad4 AMR exome

AF:

0.663

Gnomad4 ASJ exome

AF:

0.840

Gnomad4 EAS exome

AF:

0.763

Gnomad4 SAS exome

AF:

0.761

Gnomad4 FIN exome

AF:

0.843

Gnomad4 NFE exome

AF:

0.823

Gnomad4 OTH exome

AF:

0.787

GnomAD4 genome

AF:

0.706

AC:

107365

AN:

152120

Hom.:

39930

Cov.:

AF XY:

0.707

AC XY:

52562

AN XY:

74362

show subpopulations

Gnomad4 AFR

AF:

0.463

Gnomad4 AMR

AF:

0.679

Gnomad4 ASJ

AF:

0.839

Gnomad4 EAS

AF:

0.734

Gnomad4 SAS

AF:

0.767

Gnomad4 FIN

AF:

0.851

Gnomad4 NFE

AF:

0.821

Gnomad4 OTH

AF:

0.719

Alfa

AF:

0.799

Hom.:

69463

Bravo

AF:

0.681

Asia WGS

AF:

0.743

AC:

2585

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Aug 30, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.87

DANN

Benign

0.51

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over