11-116837053-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM5
The NM_000039.3(APOA1):c.148G>A(p.Gly50Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000217 in 1,614,162 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G50R) has been classified as Pathogenic.
Frequency
Consequence
NM_000039.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
APOA1 | NM_000039.3 | c.148G>A | p.Gly50Ser | missense_variant | 3/4 | ENST00000236850.5 | |
APOA1-AS | NR_126362.1 | n.123+814C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
APOA1 | ENST00000236850.5 | c.148G>A | p.Gly50Ser | missense_variant | 3/4 | 1 | NM_000039.3 | P1 | |
APOA1-AS | ENST00000669664.1 | n.74+814C>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152206Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000278 AC: 7AN: 251426Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135906
GnomAD4 exome AF: 0.0000233 AC: 34AN: 1461838Hom.: 0 Cov.: 35 AF XY: 0.0000179 AC XY: 13AN XY: 727216
GnomAD4 genome ? AF: 0.00000656 AC: 1AN: 152324Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74484
ClinVar
Submissions by phenotype
Cardiovascular phenotype Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 15, 2022 | The p.G50S variant (also known as c.148G>A), located in coding exon 2 of the APOA1 gene, results from a G to A substitution at nucleotide position 148. The glycine at codon 50 is replaced by serine, an amino acid with similar properties. This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at