16-56962068-G-C

Variant names:

• chr16-56962068-G-C
• NM_000078.3:c.89G>C

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_000078.3(CETP):​c.89G>C​(p.Cys30Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: CETP NM_000078.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.39

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 Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CETP	NM_000078.3	c.89G>C	p.Cys30Ser	missense_variant	Exon 1 of 16	ENST00000200676.8	NP_000069.2
CETP	NM_001286085.2	c.89G>C	p.Cys30Ser	missense_variant	Exon 1 of 15		NP_001273014.1
CETP	XM_006721124.4	c.89G>C	p.Cys30Ser	missense_variant	Exon 1 of 9		XP_006721187.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CETP	ENST00000200676.8	c.89G>C	p.Cys30Ser	missense_variant	Exon 1 of 16	1	NM_000078.3	ENSP00000200676.3
CETP	ENST00000379780.6	c.89G>C	p.Cys30Ser	missense_variant	Exon 1 of 15	1		ENSP00000369106.2
CETP	ENST00000569082.1	n.87G>C		non_coding_transcript_exon_variant	Exon 1 of 9	5
CETP	ENST00000566128.1	c.-306G>C		upstream_gene_variant		5		ENSP00000456276.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.74
BayesDel_addAF	Benign	-0.13	T
BayesDel_noAF	Benign	-0.42
CADD	Benign	22
DANN	Benign	0.90
DEOGEN2	Uncertain	0.67	D;.
Eigen	Benign	-0.058
Eigen_PC	Benign	-0.11
FATHMM_MKL	Benign	0.67	D
LIST_S2	Benign	0.78	T;T
M_CAP	Benign	0.044	D
MetaRNN	Uncertain	0.61	D;D
MetaSVM	Benign	-1.0	T
MutationAssessor	Uncertain	2.1	M;M
PrimateAI	Benign	0.46	T
PROVEAN	Uncertain	-3.9	D;D
REVEL	Benign	0.17
Sift	Uncertain	0.0040	D;D
Sift4G	Uncertain	0.0090	D;D
Polyphen		0.81	P;D
Vest4		0.56
MutPred		0.72		Gain of disorder (P = 0.005);Gain of disorder (P = 0.005);
MVP		0.36
MPC		0.30
ClinPred		0.95	D
GERP RS		3.1
Varity_R		0.71
gMVP		0.84

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr16-56995980;