Variant 16-56962376-G-A 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 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

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

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]

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=-0.98).

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	Effect	MANE
CETP	NM_000078.3 linkuse as main transcript	c.118+279G>A	intron_variant	ENST00000200676.8
CETP	NM_001286085.2 linkuse as main transcript	c.118+279G>A	intron_variant
CETP	XM_006721124.4 linkuse as main transcript	c.118+279G>A	intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Appris	UniProt
CETP	ENST00000200676.8 linkuse as main transcript	c.118+279G>A	intron_variant	1	NM_000078.3	P1	P11597-1
CETP	ENST00000379780.6 linkuse as main transcript	c.118+279G>A	intron_variant	1			P11597-2
CETP	ENST00000566128.1 linkuse as main transcript	c.-78+80G>A	intron_variant	5
CETP	ENST00000569082.1 linkuse as main transcript	n.116+279G>A	intron_variant, non_coding_transcript_variant	5

Frequencies

GnomAD3 genomes

AF:

0.385

AC:

58415

AN:

151616

Hom.:

11821

Cov.:

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.:

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.:

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:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

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

Coronary artery disorder

Benign:1

Benign, criteria provided, single submitter

clinical testing

Rasad Genetic Department, Rasad Pathobiology and Genetic Laboratory

May 12, 2022

- -

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.

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