chr11-116820912-C-CTCCTGCTGCTGT
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2
The NM_000482.4(APOA4):c.1145_1146insACAGCAGCAGGA(p.Gln384_Gln387dup) variant causes a inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000789 in 1,613,920 control chromosomes in the GnomAD database, including 12 homozygotes. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0044 ( 7 hom., cov: 33)
Exomes 𝑓: 0.00041 ( 5 hom. )
Consequence
APOA4
NM_000482.4 inframe_insertion
NM_000482.4 inframe_insertion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.0880
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 Likely_benign. Variant got -6 ACMG points.
BP6
?
Variant 11-116820912-C-CTCCTGCTGCTGT is Benign according to our data. Variant chr11-116820912-C-CTCCTGCTGCTGT is described in ClinVar as [Benign]. Clinvar id is 1578213.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High Homozygotes in GnomAd at 7 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
APOA4 | NM_000482.4 | c.1145_1146insACAGCAGCAGGA | p.Gln384_Gln387dup | inframe_insertion | 3/3 | ENST00000357780.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
APOA4 | ENST00000357780.5 | c.1145_1146insACAGCAGCAGGA | p.Gln384_Gln387dup | inframe_insertion | 3/3 | 1 | NM_000482.4 | P1 | |
ENST00000645414.1 | n.169-99_169-88dup | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.00440 AC: 670AN: 152106Hom.: 7 Cov.: 33
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GnomAD3 exomes AF: 0.00104 AC: 261AN: 251184Hom.: 1 AF XY: 0.000707 AC XY: 96AN XY: 135802
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GnomAD4 exome AF: 0.000410 AC: 600AN: 1461704Hom.: 5 Cov.: 66 AF XY: 0.000344 AC XY: 250AN XY: 727164
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GnomAD4 genome ? AF: 0.00442 AC: 673AN: 152216Hom.: 7 Cov.: 33 AF XY: 0.00441 AC XY: 328AN XY: 74426
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ClinVar
Significance: Benign
Submissions summary: Benign:1Other:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 20, 2023 | - - |
APOLIPOPROTEIN A-IV RARE VARIANT, APOA4*0 Other:1
other, no assertion criteria provided | literature only | OMIM | Dec 22, 2022 | - - |
Computational scores
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Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at