rs1532624

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The ENST00000200676.8(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
ENST00000200676.8 intron

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.0590
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 -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
CETPNM_000078.3 linkuse as main transcriptc.658+186C>A intron_variant ENST00000200676.8 NP_000069.2
CETPNM_001286085.2 linkuse as main transcriptc.658+186C>A intron_variant NP_001273014.1
CETPXM_006721124.4 linkuse as main transcriptc.658+186C>A intron_variant XP_006721187.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CETPENST00000200676.8 linkuse as main transcriptc.658+186C>A intron_variant 1 NM_000078.3 ENSP00000200676 P1P11597-1
CETPENST00000379780.6 linkuse as main transcriptc.658+186C>A intron_variant 1 ENSP00000369106 P11597-2
CETPENST00000566128.1 linkuse as main transcriptc.463+186C>A intron_variant 5 ENSP00000456276
CETPENST00000569082.1 linkuse as main transcriptn.760+186C>A intron_variant, non_coding_transcript_variant 5

Frequencies

GnomAD3 genomes
AF:
0.344
AC:
52339
AN:
151970
Hom.:
10332
Cov.:
33
show subpopulations
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
show subpopulations
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
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxApr 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

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

Other links and lift over

dbSNP: rs1532624; hg19: chr16-57005479; API