rs619054
Positions:
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001371904.1(APOA5):c.*31C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.222 in 1,604,378 control chromosomes in the GnomAD database, including 42,295 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.19 ( 3246 hom., cov: 33)
Exomes 𝑓: 0.23 ( 39049 hom. )
Consequence
APOA5
NM_001371904.1 3_prime_UTR
NM_001371904.1 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.411
Genes affected
APOA5 (HGNC:17288): (apolipoprotein A5) The protein encoded by this gene is an apolipoprotein that plays an important role in regulating the plasma triglyceride levels, a major risk factor for coronary artery disease. It is a component of high density lipoprotein and is highly similar to a rat protein that is upregulated in response to liver injury. Mutations in this gene have been associated with hypertriglyceridemia and hyperlipoproteinemia type 5. This gene is located proximal to the apolipoprotein gene cluster on chromosome 11q23. Alternatively spliced transcript variants encoding the same protein have been identified. [provided by RefSeq, Oct 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.78).
BP6
?
Variant 11-116790097-G-A is Benign according to our data. Variant chr11-116790097-G-A is described in ClinVar as [Benign]. Clinvar id is 1293389.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-116790097-G-A is described in Lovd as [Benign].
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.248 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
APOA5 | NM_001371904.1 | c.*31C>T | 3_prime_UTR_variant | 3/3 | ENST00000227665.9 | ||
APOA5 | NM_001166598.2 | c.*31C>T | 3_prime_UTR_variant | 4/4 | |||
APOA5 | NM_052968.5 | c.*31C>T | 3_prime_UTR_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
APOA5 | ENST00000227665.9 | c.*31C>T | 3_prime_UTR_variant | 3/3 | 1 | NM_001371904.1 | P1 | ||
APOA5 | ENST00000433069.2 | c.*31C>T | 3_prime_UTR_variant | 4/4 | 1 | P1 | |||
APOA5 | ENST00000542499.5 | c.*31C>T | 3_prime_UTR_variant | 4/4 | 5 | P1 | |||
APOA5 | ENST00000673688.1 | c.*31C>T | 3_prime_UTR_variant | 3/3 |
Frequencies
GnomAD3 genomes ? AF: 0.192 AC: 29131AN: 152104Hom.: 3240 Cov.: 33
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GnomAD3 exomes AF: 0.189 AC: 45691AN: 241740Hom.: 4918 AF XY: 0.194 AC XY: 25371AN XY: 130916
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GnomAD4 exome AF: 0.225 AC: 327237AN: 1452156Hom.: 39049 Cov.: 32 AF XY: 0.225 AC XY: 162544AN XY: 722306
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GnomAD4 genome ? AF: 0.192 AC: 29162AN: 152222Hom.: 3246 Cov.: 33 AF XY: 0.189 AC XY: 14035AN XY: 74436
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Sep 17, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at