16-56962733-GCCC-GC

Variant names:

• chr16-56962733-GCC-G
• rs34145065
• NM_000078.3:c.119-274_119-273delCC

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_000078.3(CETP):​c.119-274_119-273delCC 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
• Publications: 6 publications found

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 Gene-Disease associations (from GenCC):

• cholesterol-ester transfer protein deficiency

  Inheritance: AD Classification: STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Orphanet

ACMG classification

Our verdict: Benign. The variant received -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 VariationId is 1275353.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.445 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000078.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CETP	NM_000078.3	MANE Select	c.119-274_119-273delCC		intron	N/A	NP_000069.2	P11597-1
	CETP	NM_001286085.2		c.119-274_119-273delCC		intron	N/A	NP_001273014.1	A0A0S2Z3I8

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CETP	ENST00000200676.8	TSL:1 MANE Select	c.119-276_119-275delCC		intron	N/A	ENSP00000200676.3	P11597-1
	CETP	ENST00000379780.6	TSL:1	c.119-276_119-275delCC		intron	N/A	ENSP00000369106.2	P11597-2
	CETP	ENST00000858282.1		c.119-276_119-275delCC		intron	N/A	ENSP00000528341.1

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

African (AFR) AF: 0.196 AC: 8147 AN: 41462

American (AMR) AF: 0.407 AC: 6213 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.387 AC: 1338 AN: 3460

East Asian (EAS) AF: 0.376 AC: 1925 AN: 5126

South Asian (SAS) AF: 0.461 AC: 2217 AN: 4812

European-Finnish (FIN) AF: 0.449 AC: 4713 AN: 10488

Middle Eastern (MID) AF: 0.365 AC: 105 AN: 288

European-Non Finnish (NFE) AF: 0.433 AC: 29321 AN: 67774

Other (OTH) AF: 0.366 AC: 771 AN: 2108

Alfa AF: 0.276 Hom.: 746

Bravo AF: 0.353

Asia WGS AF: 0.403 AC: 1402 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.36
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs34145065; hg19: chr16-56996645;