rs1532624

Positions:

• chr16-56971567-C-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_000078.3(CETP):​c.658+186C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.344 in 152,090 control chromosomes in the GnomAD database, including 10,327 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.34 (10327 hom., cov: 33)
• Consequence: CETP NM_000078.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.0590

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BP6: Variant 16-56971567-C-A is Benign according to our data. Variant chr16-56971567-C-A is described in ClinVar as [Benign]. Clinvar id is 225955.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-56971567-C-A is described in Lovd as [Benign].
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.46 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CETP	NM_000078.3	c.658+186C>A		intron_variant		ENST00000200676.8	NP_000069.2
CETP	NM_001286085.2	c.658+186C>A		intron_variant			NP_001273014.1
CETP	XM_006721124.4	c.658+186C>A		intron_variant			XP_006721187.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CETP	ENST00000200676.8	c.658+186C>A		intron_variant		1	NM_000078.3	ENSP00000200676.3
CETP	ENST00000379780.6	c.658+186C>A		intron_variant		1		ENSP00000369106.2
CETP	ENST00000566128.1	c.463+186C>A		intron_variant		5		ENSP00000456276.1
CETP	ENST00000569082.1	n.760+186C>A		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.344 AC: 52339 AN: 151970 Hom.: 10332 Cov.: 33

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.525

Gnomad AMR AF: 0.344

Gnomad ASJ AF: 0.390

Gnomad EAS AF: 0.283

Gnomad SAS AF: 0.475

Gnomad FIN AF: 0.423

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.442

Gnomad OTH AF: 0.345

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

GnomAD4 genome AF: 0.344 AC: 52329 AN: 152090 Hom.: 10327 Cov.: 33 AF XY: 0.346 AC XY: 25749 AN XY: 74332

Gnomad4 AFR AF: 0.148

Gnomad4 AMR AF: 0.344

Gnomad4 ASJ AF: 0.390

Gnomad4 EAS AF: 0.283

Gnomad4 SAS AF: 0.476

Gnomad4 FIN AF: 0.423

Gnomad4 NFE AF: 0.442

Gnomad4 OTH AF: 0.341

Alfa AF: 0.421 Hom.: 15435

Bravo AF: 0.327

Asia WGS AF: 0.350 AC: 1219 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Apr 01, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	9.6
DANN	Benign	0.79

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: rs1532624; hg19: chr16-57005479;