16-56962733-GCC-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_000078.3(CETP):c.119-274_119-273del variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.36 (10969 hom., cov: 0)
• Consequence: CETP NM_000078.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.360

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]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 16-56962733-GCC-G is Benign according to our data. Variant chr16-56962733-GCC-G is described in ClinVar as [Benign]. Clinvar id is 1275353.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-56962733-GCC-G is described in Lovd as [Benign].
• BA1: GnomAd4 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
CETP	NM_000078.3	c.119-274_119-273del		intron_variant		ENST00000200676.8
CETP	NM_001286085.2	c.119-274_119-273del		intron_variant
CETP	XM_006721124.4	c.119-274_119-273del		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CETP	ENST00000200676.8	c.119-274_119-273del		intron_variant		1	NM_000078.3	P1
CETP	ENST00000379780.6	c.119-274_119-273del		intron_variant		1
CETP	ENST00000566128.1	c.-77-274_-77-273del		intron_variant		5
CETP	ENST00000569082.1	n.117-274_117-273del		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.364 AC: 55185 AN: 151578 Hom.: 10964 Cov.: 0

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.525

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.387

Gnomad EAS AF: 0.376

Gnomad SAS AF: 0.460

Gnomad FIN AF: 0.449

Gnomad MID AF: 0.384

Gnomad NFE AF: 0.433

Gnomad OTH AF: 0.368

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.364 AC: 55225 AN: 151694 Hom.: 10969 Cov.: 0 AF XY: 0.369 AC XY: 27358 AN XY: 74114

Gnomad4 AFR AF: 0.196

Gnomad4 AMR AF: 0.407

Gnomad4 ASJ AF: 0.387

Gnomad4 EAS AF: 0.376

Gnomad4 SAS AF: 0.461

Gnomad4 FIN AF: 0.449

Gnomad4 NFE AF: 0.433

Gnomad4 OTH AF: 0.366

Bravo AF: 0.353

Asia WGS AF: 0.403 AC: 1402 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 30, 2018

- -

Computational scores

Source: dbNSFP v4.3

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

Other links and lift over

dbSNP: rs34145065; hg19: chr16-56996645;