rs291044

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_000078.3(CETP):​c.982-551G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.285 in 152,016 control chromosomes in the GnomAD database, including 6,831 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 0.28 ( 6831 hom., cov: 32)

Consequence

CETP
NM_000078.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.747
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.77).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.419 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CETPNM_000078.3 linkc.982-551G>A intron_variant Intron 10 of 15 ENST00000200676.8 NP_000069.2 P11597-1A0A0S2Z3F6
CETPNM_001286085.2 linkc.802-551G>A intron_variant Intron 9 of 14 NP_001273014.1 A0A0S2Z3I8B4DMZ5

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CETPENST00000200676.8 linkc.982-551G>A intron_variant Intron 10 of 15 1 NM_000078.3 ENSP00000200676.3 P11597-1
CETPENST00000379780.6 linkc.802-551G>A intron_variant Intron 9 of 14 1 ENSP00000369106.2 P11597-2
CETPENST00000566128.1 linkc.787-551G>A intron_variant Intron 10 of 15 5 ENSP00000456276.1 H3BRJ9
CETPENST00000650358.1 linkn.829G>A non_coding_transcript_exon_variant Exon 1 of 5

Frequencies

GnomAD3 genomes
AF:
0.285
AC:
43282
AN:
151898
Hom.:
6830
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.154
Gnomad AMI
AF:
0.280
Gnomad AMR
AF:
0.309
Gnomad ASJ
AF:
0.310
Gnomad EAS
AF:
0.434
Gnomad SAS
AF:
0.237
Gnomad FIN
AF:
0.345
Gnomad MID
AF:
0.307
Gnomad NFE
AF:
0.340
Gnomad OTH
AF:
0.311
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.285
AC:
43292
AN:
152016
Hom.:
6831
Cov.:
32
AF XY:
0.285
AC XY:
21153
AN XY:
74302
show subpopulations
Gnomad4 AFR
AF:
0.154
Gnomad4 AMR
AF:
0.308
Gnomad4 ASJ
AF:
0.310
Gnomad4 EAS
AF:
0.434
Gnomad4 SAS
AF:
0.236
Gnomad4 FIN
AF:
0.345
Gnomad4 NFE
AF:
0.340
Gnomad4 OTH
AF:
0.313
Alfa
AF:
0.294
Hom.:
1270
Bravo
AF:
0.278
Asia WGS
AF:
0.318
AC:
1109
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.77
CADD
Benign
6.9
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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs291044; hg19: chr16-57011452; API