16-56962068-G-A
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Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BP6
The NM_000078.3(CETP):c.89G>A(p.Cys30Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000397 in 1,613,972 control chromosomes in the GnomAD database, including 1 homozygotes. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: 𝑓 0.000072 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000036 ( 1 hom. )
Consequence
CETP
NM_000078.3 missense
NM_000078.3 missense
Scores
2
7
10
Clinical Significance
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]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -1 ACMG points.
BP6
Variant 16-56962068-G-A is Benign according to our data. Variant chr16-56962068-G-A is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 1314022.We mark this variant Likely_benign, oryginal submissions are: {Likely_benign=1, Uncertain_significance=1}.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CETP | NM_000078.3 | c.89G>A | p.Cys30Tyr | missense_variant | 1/16 | ENST00000200676.8 | NP_000069.2 | |
CETP | NM_001286085.2 | c.89G>A | p.Cys30Tyr | missense_variant | 1/15 | NP_001273014.1 | ||
CETP | XM_006721124.4 | c.89G>A | p.Cys30Tyr | missense_variant | 1/9 | XP_006721187.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CETP | ENST00000200676.8 | c.89G>A | p.Cys30Tyr | missense_variant | 1/16 | 1 | NM_000078.3 | ENSP00000200676 | P1 | |
CETP | ENST00000379780.6 | c.89G>A | p.Cys30Tyr | missense_variant | 1/15 | 1 | ENSP00000369106 | |||
CETP | ENST00000569082.1 | n.87G>A | non_coding_transcript_exon_variant | 1/9 | 5 | |||||
CETP | ENST00000566128.1 | upstream_gene_variant | 5 | ENSP00000456276 |
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152230Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000139 AC: 35AN: 251032Hom.: 0 AF XY: 0.000103 AC XY: 14AN XY: 135720
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GnomAD4 exome AF: 0.0000363 AC: 53AN: 1461742Hom.: 1 Cov.: 31 AF XY: 0.0000248 AC XY: 18AN XY: 727178
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GnomAD4 genome AF: 0.0000723 AC: 11AN: 152230Hom.: 0 Cov.: 32 AF XY: 0.0000807 AC XY: 6AN XY: 74384
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ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:1Benign:1
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
not provided Uncertain:1Benign:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Jan 19, 2021 | Has not been previously published as pathogenic or benign to our knowledge; In silico analysis supports that this missense variant has a deleterious effect on protein structure/function - |
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Nov 01, 2023 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
DEOGEN2
Uncertain
D;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
D
LIST_S2
Benign
T;D
M_CAP
Benign
D
MetaRNN
Uncertain
T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;M
MutationTaster
Benign
D;D
PrimateAI
Uncertain
T
PROVEAN
Pathogenic
D;D
REVEL
Benign
Sift
Uncertain
D;D
Sift4G
Uncertain
T;T
Polyphen
D;D
Vest4
MutPred
Gain of catalytic residue at C30 (P = 0.098);Gain of catalytic residue at C30 (P = 0.098);
MVP
MPC
ClinPred
D
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Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at