Variant 16-56978024-C-T 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.982-67C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0283 in 1,578,790 control chromosomes in the GnomAD database, including 2,344 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.072 ( 882 hom., cov: 32)

Exomes 𝑓: 0.024 ( 1462 hom. )

Consequence

CETP
NM_000078.3 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -3.12

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=-0.9).

BP6

Variant 16-56978024-C-T is Benign according to our data. Variant chr16-56978024-C-T is described in ClinVar as [Benign]. Clinvar id is 1228339.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.18 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.982-67C>T		intron_variant		ENST00000200676.8	NP_000069.2
CETP	NM_001286085.2 linkuse as main transcript	c.802-67C>T		intron_variant			NP_001273014.1

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CETP	ENST00000200676.8 linkuse as main transcript	c.982-67C>T	intron_variant		1	NM_000078.3	ENSP00000200676	P1	P11597-1
CETP	ENST00000379780.6 linkuse as main transcript	c.802-67C>T	intron_variant		1		ENSP00000369106		P11597-2
CETP	ENST00000566128.1 linkuse as main transcript	c.787-67C>T	intron_variant		5		ENSP00000456276
CETP	ENST00000650358.1 linkuse as main transcript	n.1313C>T	non_coding_transcript_exon_variant	1/5

Frequencies

GnomAD3 genomes

AF:

0.0719

AC:

10936

AN:

152102

Hom.:

879

Cov.:

show subpopulations

Gnomad AFR

AF:

0.183

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0932

Gnomad ASJ

AF:

0.00461

Gnomad EAS

AF:

0.126

Gnomad SAS

AF:

0.0532

Gnomad FIN

AF:

0.0164

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0103

Gnomad OTH

AF:

0.0608

GnomAD4 exome

AF:

0.0237

AC:

33771

AN:

1426570

Hom.:

1462

AF XY:

0.0236

AC XY:

16680

AN XY:

707036

show subpopulations

Gnomad4 AFR exome

AF:

0.190

Gnomad4 AMR exome

AF:

0.118

Gnomad4 ASJ exome

AF:

0.00624

Gnomad4 EAS exome

AF:

0.118

Gnomad4 SAS exome

AF:

0.0495

Gnomad4 FIN exome

AF:

0.0172

Gnomad4 NFE exome

AF:

0.00991

Gnomad4 OTH exome

AF:

0.0326

GnomAD4 genome

AF:

0.0721

AC:

10969

AN:

152220

Hom.:

882

Cov.:

AF XY:

0.0721

AC XY:

5370

AN XY:

74442

show subpopulations

Gnomad4 AFR

AF:

0.183

Gnomad4 AMR

AF:

0.0937

Gnomad4 ASJ

AF:

0.00461

Gnomad4 EAS

AF:

0.125

Gnomad4 SAS

AF:

0.0532

Gnomad4 FIN

AF:

0.0164

Gnomad4 NFE

AF:

0.0103

Gnomad4 OTH

AF:

0.0620

Alfa

AF:

0.0290

Hom.:

175

Bravo

AF:

0.0851

Asia WGS

AF:

0.0980

AC:

340

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	Apr 08, 2019	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.064

DANN

Benign

0.59

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