chr11-116820918-C-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_000482.4(APOA4):c.1140G>T(p.Gln380His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.073 in 1,614,064 control chromosomes in the GnomAD database, including 4,952 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_000482.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
APOA4 | NM_000482.4 | c.1140G>T | p.Gln380His | missense_variant | 3/3 | ENST00000357780.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
APOA4 | ENST00000357780.5 | c.1140G>T | p.Gln380His | missense_variant | 3/3 | 1 | NM_000482.4 | P1 | |
ENST00000645414.1 | n.169-102C>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0519 AC: 7905AN: 152210Hom.: 306 Cov.: 33
GnomAD3 exomes AF: 0.0523 AC: 13128AN: 251086Hom.: 470 AF XY: 0.0528 AC XY: 7162AN XY: 135722
GnomAD4 exome AF: 0.0752 AC: 109875AN: 1461736Hom.: 4646 Cov.: 67 AF XY: 0.0730 AC XY: 53054AN XY: 727142
GnomAD4 genome ? AF: 0.0519 AC: 7904AN: 152328Hom.: 306 Cov.: 33 AF XY: 0.0483 AC XY: 3600AN XY: 74480
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 04, 2021 | This variant is associated with the following publications: (PMID: 9714133, 20117098, 1349197) - |
APOLIPOPROTEIN A-IV POLYMORPHISM, APOA4*1/APOA4*2 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | May 01, 1992 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at