1-161223055-CCACACACACACACACACACACACA-CCACACACACACACACACACACACACACA
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP6BS2_Supporting
The NM_001643.2(APOA2):c.53-9_53-6dupTGTG variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: 𝑓 0.0086 ( 10 hom., cov: 0)
Exomes 𝑓: 0.0065 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
APOA2
NM_001643.2 splice_region, intron
NM_001643.2 splice_region, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.116
Genes affected
APOA2 (HGNC:601): (apolipoprotein A2) This gene encodes apolipoprotein (apo-) A-II, which is the second most abundant protein of the high density lipoprotein particles. The protein is found in plasma as a monomer, homodimer, or heterodimer with apolipoprotein D. Defects in this gene may result in apolipoprotein A-II deficiency or hypercholesterolemia. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
BP6
Variant 1-161223055-C-CCACA is Benign according to our data. Variant chr1-161223055-C-CCACA is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 293293.We mark this variant Likely_benign, oryginal submissions are: {Uncertain_significance=1, Benign=1, Likely_benign=1}.
BS2
High Homozygotes in GnomAd4 at 10 AR geneVariant has number of homozygotes lower than other variant known as pathogenic in the gene, so the strength is limited to Supporting.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
APOA2 | ENST00000367990.7 | c.53-9_53-6dupTGTG | splice_region_variant, intron_variant | Intron 2 of 3 | 1 | NM_001643.2 | ENSP00000356969.3 | |||
APOA2 | ENST00000470459.6 | c.53-9_53-6dupTGTG | splice_region_variant, intron_variant | Intron 2 of 4 | 5 | ENSP00000477031.1 |
Frequencies
GnomAD3 genomes AF: 0.00858 AC: 1266AN: 147508Hom.: 10 Cov.: 0
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00651 AC: 9344AN: 1436274Hom.: 0 Cov.: 0 AF XY: 0.00676 AC XY: 4830AN XY: 714690
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GnomAD4 genome AF: 0.00857 AC: 1265AN: 147620Hom.: 10 Cov.: 0 AF XY: 0.00892 AC XY: 640AN XY: 71724
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ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:1Benign:4
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
not provided Benign:3
-
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Significance: Likely benign
Review Status: no assertion criteria provided
Collection Method: clinical testing
- -
Dec 31, 2019
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
- -
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Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center
Significance: Likely benign
Review Status: no assertion criteria provided
Collection Method: clinical testing
- -
Apolipoprotein A-II deficiency Uncertain:1
Jun 14, 2016
Illumina Laboratory Services, Illumina
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing
- -
not specified Benign:1
Dec 22, 2021
Genetic Services Laboratory, University of Chicago
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
- -
Computational scores
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Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at