16-56968820-T-G

Position:

• chr16-56968820-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000078.3(CETP):​c.234-566T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.753 in 150,930 control chromosomes in the GnomAD database, including 43,149 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 0.75 (43149 hom., cov: 27)
• Consequence: CETP NM_000078.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.506

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.847 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CETP	NM_000078.3	c.234-566T>G		intron_variant		ENST00000200676.8	NP_000069.2
CETP	NM_001286085.2	c.234-566T>G		intron_variant			NP_001273014.1
CETP	XM_006721124.4	c.234-566T>G		intron_variant			XP_006721187.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CETP	ENST00000200676.8	c.234-566T>G		intron_variant		1	NM_000078.3	ENSP00000200676.3
CETP	ENST00000379780.6	c.234-566T>G		intron_variant		1		ENSP00000369106.2
CETP	ENST00000566128.1	c.39-566T>G		intron_variant		5		ENSP00000456276.1
CETP	ENST00000569082.1	n.232-566T>G		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.753 AC: 113564 AN: 150814 Hom.: 43124 Cov.: 27

Gnomad AFR AF: 0.657

Gnomad AMI AF: 0.893

Gnomad AMR AF: 0.752

Gnomad ASJ AF: 0.824

Gnomad EAS AF: 0.869

Gnomad SAS AF: 0.789

Gnomad FIN AF: 0.780

Gnomad MID AF: 0.801

Gnomad NFE AF: 0.790

Gnomad OTH AF: 0.757

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

GnomAD4 genome AF: 0.753 AC: 113636 AN: 150930 Hom.: 43149 Cov.: 27 AF XY: 0.754 AC XY: 55490 AN XY: 73628

Gnomad4 AFR AF: 0.657

Gnomad4 AMR AF: 0.752

Gnomad4 ASJ AF: 0.824

Gnomad4 EAS AF: 0.869

Gnomad4 SAS AF: 0.789

Gnomad4 FIN AF: 0.780

Gnomad4 NFE AF: 0.790

Gnomad4 OTH AF: 0.758

Alfa AF: 0.793 Hom.: 87306

Bravo AF: 0.748

Asia WGS AF: 0.817 AC: 2840 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
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: rs9939224; hg19: chr16-57002732;