rs41338746
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001371904.1(APOA5):c.49+55G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00856 in 1,613,600 control chromosomes in the GnomAD database, including 873 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.043 ( 445 hom., cov: 34)
Exomes 𝑓: 0.0050 ( 428 hom. )
Consequence
APOA5
NM_001371904.1 intron
NM_001371904.1 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.420
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=-0.83).
BP6
?
Variant 11-116791757-C-A is Benign according to our data. Variant chr11-116791757-C-A is described in ClinVar as [Benign]. Clinvar id is 1252218.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.144 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
APOA5 | NM_001371904.1 | c.49+55G>T | intron_variant | ENST00000227665.9 | |||
APOA5 | NM_001166598.2 | c.49+55G>T | intron_variant | ||||
APOA5 | NM_052968.5 | c.49+55G>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
APOA5 | ENST00000227665.9 | c.49+55G>T | intron_variant | 1 | NM_001371904.1 | P1 | |||
APOA5 | ENST00000433069.2 | c.49+55G>T | intron_variant | 1 | P1 | ||||
APOA5 | ENST00000542499.5 | c.49+55G>T | intron_variant | 5 | P1 | ||||
APOA5 | ENST00000673688.1 | c.49+55G>T | intron_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0430 AC: 6537AN: 152186Hom.: 445 Cov.: 34
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GnomAD4 exome AF: 0.00497 AC: 7263AN: 1461296Hom.: 428 Cov.: 33 AF XY: 0.00444 AC XY: 3224AN XY: 726920
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GnomAD4 genome ? AF: 0.0430 AC: 6549AN: 152304Hom.: 445 Cov.: 34 AF XY: 0.0418 AC XY: 3112AN XY: 74482
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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 | Apr 07, 2019 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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