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

Scores

Not classified

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:1B:4

Conservation

PhyloP100: 0.116
Variant links:
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]

Genome browser will be placed here

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

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
APOA2NM_001643.2 linkc.53-9_53-6dupTGTG splice_region_variant, intron_variant Intron 2 of 3 ENST00000367990.7 NP_001634.1 P02652

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
APOA2ENST00000367990.7 linkc.53-9_53-6dupTGTG splice_region_variant, intron_variant Intron 2 of 3 1 NM_001643.2 ENSP00000356969.3 P02652
APOA2ENST00000470459.6 linkc.53-9_53-6dupTGTG splice_region_variant, intron_variant Intron 2 of 4 5 ENSP00000477031.1 V9GYS1

Frequencies

GnomAD3 genomes
AF:
0.00858
AC:
1266
AN:
147508
Hom.:
10
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.00979
Gnomad AMI
AF:
0.00111
Gnomad AMR
AF:
0.00672
Gnomad ASJ
AF:
0.0168
Gnomad EAS
AF:
0.000604
Gnomad SAS
AF:
0.00997
Gnomad FIN
AF:
0.00807
Gnomad MID
AF:
0.00955
Gnomad NFE
AF:
0.00861
Gnomad OTH
AF:
0.00592
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
0.00651
AC:
9344
AN:
1436274
Hom.:
0
Cov.:
0
AF XY:
0.00676
AC XY:
4830
AN XY:
714690
show subpopulations
Gnomad4 AFR exome
AF:
0.00659
Gnomad4 AMR exome
AF:
0.00434
Gnomad4 ASJ exome
AF:
0.00992
Gnomad4 EAS exome
AF:
0.000255
Gnomad4 SAS exome
AF:
0.00935
Gnomad4 FIN exome
AF:
0.00581
Gnomad4 NFE exome
AF:
0.00651
Gnomad4 OTH exome
AF:
0.00668
GnomAD4 genome
AF:
0.00857
AC:
1265
AN:
147620
Hom.:
10
Cov.:
0
AF XY:
0.00892
AC XY:
640
AN XY:
71724
show subpopulations
Gnomad4 AFR
AF:
0.00979
Gnomad4 AMR
AF:
0.00664
Gnomad4 ASJ
AF:
0.0168
Gnomad4 EAS
AF:
0.000605
Gnomad4 SAS
AF:
0.00998
Gnomad4 FIN
AF:
0.00807
Gnomad4 NFE
AF:
0.00861
Gnomad4 OTH
AF:
0.00586

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

- -

-
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

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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: rs17244502; hg19: chr1-161192845; API