Variant 16-56973534-T-G 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.930+24T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.191 in 1,612,826 control chromosomes in the GnomAD database, including 32,944 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.25 ( 5978 hom., cov: 32)

Exomes 𝑓: 0.18 ( 26966 hom. )

Consequence

CETP
NM_000078.3 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.0470

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:

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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=-0.85).

BP6

Variant 16-56973534-T-G is Benign according to our data. Variant chr16-56973534-T-G is described in ClinVar as [Benign]. Clinvar id is 1267902.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-56973534-T-G is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.415 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+24T>G		intron_variant		ENST00000200676.8	NP_000069.2
CETP	NM_001286085.2 linkuse as main transcript	c.750+1451T>G		intron_variant			NP_001273014.1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	Appris	UniProt
CETP	ENST00000200676.8 linkuse as main transcript	c.930+24T>G	intron_variant	1	NM_000078.3	ENSP00000200676	P1	P11597-1
CETP	ENST00000379780.6 linkuse as main transcript	c.750+1451T>G	intron_variant	1		ENSP00000369106		P11597-2
CETP	ENST00000566128.1 linkuse as main transcript	c.735+24T>G	intron_variant	5		ENSP00000456276

Frequencies

GnomAD3 genomes

AF:

0.255

AC:

38692

AN:

151894

Hom.:

5961

Cov.:

show subpopulations

Gnomad AFR

AF:

0.420

Gnomad AMI

AF:

0.112

Gnomad AMR

AF:

0.301

Gnomad ASJ

AF:

0.155

Gnomad EAS

AF:

0.266

Gnomad SAS

AF:

0.214

Gnomad FIN

AF:

0.147

Gnomad MID

AF:

0.213

Gnomad NFE

AF:

0.170

Gnomad OTH

AF:

0.254

GnomAD3 exomes

AF:

0.221

AC:

55240

AN:

249762

Hom.:

6960

AF XY:

0.214

AC XY:

28917

AN XY:

135048

show subpopulations

Gnomad AFR exome

AF:

0.424

Gnomad AMR exome

AF:

0.329

Gnomad ASJ exome

AF:

0.152

Gnomad EAS exome

AF:

0.279

Gnomad SAS exome

AF:

0.224

Gnomad FIN exome

AF:

0.156

Gnomad NFE exome

AF:

0.169

Gnomad OTH exome

AF:

0.189

GnomAD4 exome

AF:

0.184

AC:

268841

AN:

1460812

Hom.:

26966

Cov.:

AF XY:

0.184

AC XY:

133435

AN XY:

726698

show subpopulations

Gnomad4 AFR exome

AF:

0.427

Gnomad4 AMR exome

AF:

0.325

Gnomad4 ASJ exome

AF:

0.154

Gnomad4 EAS exome

AF:

0.237

Gnomad4 SAS exome

AF:

0.220

Gnomad4 FIN exome

AF:

0.154

Gnomad4 NFE exome

AF:

0.168

Gnomad4 OTH exome

AF:

0.197

GnomAD4 genome

AF:

0.255

AC:

38752

AN:

152014

Hom.:

5978

Cov.:

AF XY:

0.255

AC XY:

18919

AN XY:

74288

show subpopulations

Gnomad4 AFR

AF:

0.420

Gnomad4 AMR

AF:

0.302

Gnomad4 ASJ

AF:

0.155

Gnomad4 EAS

AF:

0.266

Gnomad4 SAS

AF:

0.214

Gnomad4 FIN

AF:

0.147

Gnomad4 NFE

AF:

0.170

Gnomad4 OTH

AF:

0.253

Alfa

AF:

0.138

Hom.:

429

Bravo

AF:

0.276

Asia WGS

AF:

0.234

AC:

813

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

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

2.3

DANN

Benign

0.69

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