rs17244502
Variant names:
Your query was ambiguous. Multiple possible variants found:
- chr1-161223055-CCACACACACACACACACACACACA-C
- chr1-161223055-CCACACACACACACACACACACACA-CCA
- chr1-161223055-CCACACACACACACACACACACACA-CCACACA
- chr1-161223055-CCACACACACACACACACACACACA-CCACACACA
- chr1-161223055-CCACACACACACACACACACACACA-CCACACACACA
- chr1-161223055-CCACACACACACACACACACACACA-CCACACACACACA
- chr1-161223055-CCACACACACACACACACACACACA-CCACACACACACACA
- chr1-161223055-CCACACACACACACACACACACACA-CCACACACACACACACA
- chr1-161223055-CCACACACACACACACACACACACA-CCACACACACACACACACA
- chr1-161223055-CCACACACACACACACACACACACA-CCACACACACACACACACACA
- chr1-161223055-CCACACACACACACACACACACACA-CCACACACACACACACACACACA
- chr1-161223055-CCACACACACACACACACACACACA-CCACACACACACACACACACACACACA
- chr1-161223055-CCACACACACACACACACACACACA-CCACACACACACACACACACACACACACA
- chr1-161223055-CCACACACACACACACACACACACA-CCACACACACACACACACACACACACACACA
- chr1-161223055-CCACACACACACACACACACACACA-CCACACACACACACACACACACACACACACACA
- chr1-161223055-CCACACACACACACACACACACACA-CCACACACACACACACACACACACACACACACACA
- chr1-161223055-CCACACACACACACACACACACACA-CCACACACACACACACACACACACACACACACACACA
- chr1-161223055-CCACACACACACACACACACACACA-CCACACACACACACACACACACACACACACACACACACACA
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001643.2(APOA2):c.53-29_53-6delTGTGTGTGTGTGTGTGTGTGTGTG variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000944 in 1,588,304 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000014 ( 0 hom., cov: 0)
Exomes 𝑓: 0.0000090 ( 0 hom. )
Consequence
APOA2
NM_001643.2 splice_region, intron
NM_001643.2 splice_region, intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.506
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 Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
APOA2 | ENST00000367990.7 | c.53-29_53-6delTGTGTGTGTGTGTGTGTGTGTGTG | splice_region_variant, intron_variant | Intron 2 of 3 | 1 | NM_001643.2 | ENSP00000356969.3 | |||
APOA2 | ENST00000470459.6 | c.53-29_53-6delTGTGTGTGTGTGTGTGTGTGTGTG | splice_region_variant, intron_variant | Intron 2 of 4 | 5 | ENSP00000477031.1 |
Frequencies
GnomAD3 genomes AF: 0.0000136 AC: 2AN: 147528Hom.: 0 Cov.: 0
GnomAD3 genomes
AF:
AC:
2
AN:
147528
Hom.:
Cov.:
0
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.00000902 AC: 13AN: 1440776Hom.: 0 AF XY: 0.00000837 AC XY: 6AN XY: 716844
GnomAD4 exome
AF:
AC:
13
AN:
1440776
Hom.:
AF XY:
AC XY:
6
AN XY:
716844
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.0000136 AC: 2AN: 147528Hom.: 0 Cov.: 0 AF XY: 0.0000140 AC XY: 1AN XY: 71606
GnomAD4 genome
AF:
AC:
2
AN:
147528
Hom.:
Cov.:
0
AF XY:
AC XY:
1
AN XY:
71606
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at