rs11076175

chr16-56972466-A-G

Variant summary

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

The NM_000078.3(CETP):c.750+383A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.197 in 152,224 control chromosomes in the GnomAD database, including 3,147 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 0.20 (3147 hom., cov: 33)
• Consequence: CETP NM_000078.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.553

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.244 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CETP	NM_000078.3	c.750+383A>G		intron_variant		ENST00000200676.8
CETP	XM_006721124.4	c.*247A>G		3_prime_UTR_variant	9/9
CETP	NM_001286085.2	c.750+383A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CETP	ENST00000200676.8	c.750+383A>G		intron_variant		1	NM_000078.3	P1
CETP	ENST00000379780.6	c.750+383A>G		intron_variant		1
CETP	ENST00000566128.1	c.555+383A>G		intron_variant		5
CETP	ENST00000569082.1	n.852+383A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.197 AC: 30011 AN: 152106 Hom.: 3142 Cov.: 33

Gnomad AFR AF: 0.248

Gnomad AMI AF: 0.0440

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.180

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.197 AC: 30036 AN: 152224 Hom.: 3147 Cov.: 33 AF XY: 0.197 AC XY: 14636 AN XY: 74438

Gnomad4 AFR AF: 0.248

Gnomad4 AMR AF: 0.214

Gnomad4 ASJ AF: 0.150

Gnomad4 EAS AF: 0.110

Gnomad4 SAS AF: 0.190

Gnomad4 FIN AF: 0.164

Gnomad4 NFE AF: 0.180

Gnomad4 OTH AF: 0.199

Alfa AF: 0.197 Hom.: 578

Bravo AF: 0.202

Asia WGS AF: 0.153 AC: 531 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.89
Dann	Benign	0.33

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: rs11076175; hg19: chr16-57006378;