chr11-116820795-GGACA-G
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_000482.4(APOA4):c.*68_*71del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.489 in 1,577,418 control chromosomes in the GnomAD database, including 197,947 homozygotes. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.39 ( 13398 hom., cov: 0)
Exomes 𝑓: 0.50 ( 184549 hom. )
Consequence
APOA4
NM_000482.4 3_prime_UTR
NM_000482.4 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.937
Genes affected
APOA4 (HGNC:602): (apolipoprotein A4) Apoliprotein (apo) A-IV gene contains 3 exons separated by two introns. A sequence polymorphism has been identified in the 3'UTR of the third exon. The primary translation product is a 396-residue preprotein which after proteolytic processing is secreted its primary site of synthesis, the intestine, in association with chylomicron particles. Although its precise function is not known, apo A-IV is a potent activator of lecithin-cholesterol acyltransferase in vitro. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
?
Variant 11-116820795-GGACA-G is Benign according to our data. Variant chr11-116820795-GGACA-G is described in ClinVar as [Benign]. Clinvar id is 1238294.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.519 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
APOA4 | NM_000482.4 | c.*68_*71del | 3_prime_UTR_variant | 3/3 | ENST00000357780.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
APOA4 | ENST00000357780.5 | c.*68_*71del | 3_prime_UTR_variant | 3/3 | 1 | NM_000482.4 | P1 | ||
ENST00000645414.1 | n.165_168del | non_coding_transcript_exon_variant | 1/2 |
Frequencies
GnomAD3 genomes ? AF: 0.387 AC: 58724AN: 151762Hom.: 13406 Cov.: 0
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GnomAD4 exome AF: 0.500 AC: 712397AN: 1425540Hom.: 184549 AF XY: 0.494 AC XY: 348997AN XY: 705810
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GnomAD4 genome ? AF: 0.387 AC: 58715AN: 151878Hom.: 13398 Cov.: 0 AF XY: 0.381 AC XY: 28251AN XY: 74240
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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 | May 10, 2021 | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at