rs11508026

chr16-56965416-C-T

Variant summary

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

The NM_000078.3(CETP):c.233+2292C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.325 in 151,346 control chromosomes in the GnomAD database, including 9,685 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 0.33 (9685 hom., cov: 32)
• Consequence: CETP NM_000078.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.437 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CETP	NM_000078.3	c.233+2292C>T		intron_variant		ENST00000200676.8
CETP	NM_001286085.2	c.233+2292C>T		intron_variant
CETP	XM_006721124.4	c.233+2292C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CETP	ENST00000200676.8	c.233+2292C>T		intron_variant		1	NM_000078.3	P1
CETP	ENST00000379780.6	c.233+2292C>T		intron_variant		1
CETP	ENST00000566128.1	c.38+2292C>T		intron_variant		5
CETP	ENST00000569082.1	n.231+2292C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.325 AC: 49212 AN: 151228 Hom.: 9690 Cov.: 32

Gnomad AFR AF: 0.0969

Gnomad AMI AF: 0.529

Gnomad AMR AF: 0.332

Gnomad ASJ AF: 0.390

Gnomad EAS AF: 0.286

Gnomad SAS AF: 0.452

Gnomad FIN AF: 0.423

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.434

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.325 AC: 49203 AN: 151346 Hom.: 9685 Cov.: 32 AF XY: 0.328 AC XY: 24243 AN XY: 73924

Gnomad4 AFR AF: 0.0966

Gnomad4 AMR AF: 0.332

Gnomad4 ASJ AF: 0.390

Gnomad4 EAS AF: 0.286

Gnomad4 SAS AF: 0.453

Gnomad4 FIN AF: 0.423

Gnomad4 NFE AF: 0.434

Gnomad4 OTH AF: 0.329

Alfa AF: 0.361 Hom.: 2548

Bravo AF: 0.304

Asia WGS AF: 0.343 AC: 1193 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	0.44
Dann	Benign	0.50

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: rs11508026; hg19: chr16-56999328;