NM_000078.3:c.751-414T>A

Variant names:

• chr16-56972917-T-A
• rs289713
• NM_000078.3:c.751-414T>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000078.3(CETP):​c.751-414T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.703 in 151,814 control chromosomes in the GnomAD database, including 39,069 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.70 (39069 hom., cov: 30)
• Consequence: CETP NM_000078.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.749
• Publications: 19 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: Orphanet, Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.803 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CETP	NM_000078.3	c.751-414T>A		intron_variant	Intron 8 of 15	ENST00000200676.8	NP_000069.2
CETP	NM_001286085.2	c.750+834T>A		intron_variant	Intron 8 of 14		NP_001273014.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CETP	ENST00000200676.8	c.751-414T>A		intron_variant	Intron 8 of 15	1	NM_000078.3	ENSP00000200676.3
CETP	ENST00000379780.6	c.750+834T>A		intron_variant	Intron 8 of 14	1		ENSP00000369106.2
CETP	ENST00000566128.1	c.556-414T>A		intron_variant	Intron 8 of 15	5		ENSP00000456276.1
CETP	ENST00000569082.1	n.853-414T>A		intron_variant	Intron 8 of 8	5

Frequencies

GnomAD3 genomes AF: 0.703 AC: 106706 AN: 151696 Hom.: 39074 Cov.: 30

Gnomad AFR AF: 0.483

Gnomad AMI AF: 0.886

Gnomad AMR AF: 0.676

Gnomad ASJ AF: 0.842

Gnomad EAS AF: 0.747

Gnomad SAS AF: 0.766

Gnomad FIN AF: 0.809

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.809

Gnomad OTH AF: 0.713

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

GnomAD4 genome AF: 0.703 AC: 106733 AN: 151814 Hom.: 39069 Cov.: 30 AF XY: 0.704 AC XY: 52204 AN XY: 74196

African (AFR) AF: 0.483 AC: 19948 AN: 41318

American (AMR) AF: 0.676 AC: 10302 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.842 AC: 2923 AN: 3470

East Asian (EAS) AF: 0.747 AC: 3851 AN: 5154

South Asian (SAS) AF: 0.767 AC: 3692 AN: 4816

European-Finnish (FIN) AF: 0.809 AC: 8519 AN: 10536

Middle Eastern (MID) AF: 0.799 AC: 235 AN: 294

European-Non Finnish (NFE) AF: 0.809 AC: 54955 AN: 67966

Other (OTH) AF: 0.712 AC: 1500 AN: 2106

Alfa AF: 0.747 Hom.: 5122

Bravo AF: 0.683

Asia WGS AF: 0.742 AC: 2580 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.56
DANN	Benign	0.25
PhyloP100		-0.75
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: rs289713; hg19: chr16-57006829;