11-116836134-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 1P and 0B. PP5
The NM_000039.3(APOA1):c.478G>A(p.Glu160Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000026 in 1,612,866 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E160D) has been classified as Uncertain significance.
Frequency
Consequence
NM_000039.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
APOA1 | NM_000039.3 | c.478G>A | p.Glu160Lys | missense_variant | 4/4 | ENST00000236850.5 | |
APOA1-AS | NR_126362.1 | n.18C>T | non_coding_transcript_exon_variant | 1/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
APOA1 | ENST00000236850.5 | c.478G>A | p.Glu160Lys | missense_variant | 4/4 | 1 | NM_000039.3 | P1 | |
APOA1-AS | ENST00000669664.1 | upstream_gene_variant |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152216Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000200 AC: 5AN: 249720Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135328
GnomAD4 exome AF: 0.0000281 AC: 41AN: 1460650Hom.: 0 Cov.: 32 AF XY: 0.0000344 AC XY: 25AN XY: 726682
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152216Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74364
ClinVar
Submissions by phenotype
APOLIPOPROTEIN A-I (NORWAY) Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Aug 25, 1984 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at