11-116835789-G-C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_000039.3(APOA1):c.*19C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000386 in 1,613,034 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_000039.3 3_prime_UTR
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
APOA1 | NM_000039.3 | c.*19C>G | 3_prime_UTR_variant | Exon 4 of 4 | ENST00000236850.5 | NP_000030.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000387 AC: 59AN: 152268Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.000648 AC: 159AN: 245468Hom.: 2 AF XY: 0.000774 AC XY: 104AN XY: 134420
GnomAD4 exome AF: 0.000385 AC: 563AN: 1460650Hom.: 4 Cov.: 32 AF XY: 0.000500 AC XY: 363AN XY: 726642
GnomAD4 genome AF: 0.000387 AC: 59AN: 152384Hom.: 1 Cov.: 33 AF XY: 0.000523 AC XY: 39AN XY: 74524
ClinVar
Submissions by phenotype
Familial visceral amyloidosis, Ostertag type Benign:2
- -
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
not specified Benign:1
- -
Hypoalphalipoproteinemia, primary, 2, intermediate Benign:1
- -
Hypoalphalipoproteinemia, primary, 2 Benign:1
- -
Hypoalphalipoproteinemia, primary, 1 Benign:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at