16-56977331-C-T

Position:

• chr16-56977331-C-T

Variant summary

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

The ENST00000200676.8(CETP):​c.982-760C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0583 in 152,180 control chromosomes in the GnomAD database, including 366 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 0.058 (366 hom., cov: 32)
• Consequence: CETP ENST00000200676.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.37

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=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.102 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CETP	NM_000078.3	c.982-760C>T		intron_variant		ENST00000200676.8	NP_000069.2
CETP	NM_001286085.2	c.802-760C>T		intron_variant			NP_001273014.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CETP	ENST00000200676.8	c.982-760C>T		intron_variant		1	NM_000078.3	ENSP00000200676	P1
CETP	ENST00000379780.6	c.802-760C>T		intron_variant		1		ENSP00000369106
CETP	ENST00000566128.1	c.787-760C>T		intron_variant		5		ENSP00000456276
CETP	ENST00000650358.1	n.620C>T		non_coding_transcript_exon_variant	1/5

Frequencies

GnomAD3 genomes AF: 0.0583 AC: 8868 AN: 152062 Hom.: 364 Cov.: 32

Gnomad AFR AF: 0.0172

Gnomad AMI AF: 0.0418

Gnomad AMR AF: 0.0430

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.102

Gnomad SAS AF: 0.110

Gnomad FIN AF: 0.0812

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0735

Gnomad OTH AF: 0.0718

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

GnomAD4 genome AF: 0.0583 AC: 8874 AN: 152180 Hom.: 366 Cov.: 32 AF XY: 0.0593 AC XY: 4410 AN XY: 74410

Gnomad4 AFR AF: 0.0173

Gnomad4 AMR AF: 0.0430

Gnomad4 ASJ AF: 0.101

Gnomad4 EAS AF: 0.102

Gnomad4 SAS AF: 0.110

Gnomad4 FIN AF: 0.0812

Gnomad4 NFE AF: 0.0736

Gnomad4 OTH AF: 0.0735

Alfa AF: 0.0694 Hom.: 506

Bravo AF: 0.0525

Asia WGS AF: 0.117 AC: 405 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.20
DANN	Benign	0.87

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: rs12720898; hg19: chr16-57011243;