11-116789838-CCT-C

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP6

The NM_001371904.1(APOA5):​c.*288_*289delAG variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in Lovd as Benign (no stars).

Frequency

Genomes: not found (cov: 32)

Consequence

APOA5
NM_001371904.1 3_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.265
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP6
Variant 11-116789838-CCT-C is Benign according to our data. Variant chr11-116789838-CCT-C is described in Lovd as [Benign].

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
APOA5NM_001371904.1 linkc.*288_*289delAG 3_prime_UTR_variant Exon 3 of 3 ENST00000227665.9 NP_001358833.1
APOA5NM_001166598.2 linkc.*288_*289delAG 3_prime_UTR_variant Exon 4 of 4 NP_001160070.1 Q6Q788A0A0B4RUS7
APOA5NM_052968.5 linkc.*288_*289delAG 3_prime_UTR_variant Exon 4 of 4 NP_443200.2 Q6Q788A0A0B4RUS7

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
APOA5ENST00000227665 linkc.*288_*289delAG 3_prime_UTR_variant Exon 3 of 3 1 NM_001371904.1 ENSP00000227665.4 Q6Q788
APOA5ENST00000542499 linkc.*288_*289delAG 3_prime_UTR_variant Exon 4 of 4 5 ENSP00000445002.1 Q6Q788

Frequencies

GnomAD3 genomes
Cov.:
32
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr11-116660554; API