rs289713

chr16-56972917-T-Achr16-56972917-T-G

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP6 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. Variant has been reported in Lovd as Benign (no stars).

• 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

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 -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BP6: Variant 16-56972917-T-A is Benign according to our data. Variant chr16-56972917-T-A is described in Lovd as [Benign].
• 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/exons	MANE	UniProt
CETP	NM_000078.3	c.751-414T>A		intron_variant		ENST00000200676.8
CETP	NM_001286085.2	c.750+834T>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CETP	ENST00000200676.8	c.751-414T>A		intron_variant		1	NM_000078.3	P1
CETP	ENST00000379780.6	c.750+834T>A		intron_variant		1
CETP	ENST00000566128.1	c.556-414T>A		intron_variant		5
CETP	ENST00000569082.1	n.853-414T>A		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.483

Gnomad4 AMR AF: 0.676

Gnomad4 ASJ AF: 0.842

Gnomad4 EAS AF: 0.747

Gnomad4 SAS AF: 0.767

Gnomad4 FIN AF: 0.809

Gnomad4 NFE AF: 0.809

Gnomad4 OTH AF: 0.712

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

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: rs289713; hg19: chr16-57006829;