chr11-116820959-T-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_000482.4(APOA4):āc.1099A>Gā(p.Thr367Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00124 in 1,613,728 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T367S) has been classified as Benign.
Frequency
Consequence
NM_000482.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
APOA4 | NM_000482.4 | c.1099A>G | p.Thr367Ala | missense_variant | 3/3 | ENST00000357780.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
APOA4 | ENST00000357780.5 | c.1099A>G | p.Thr367Ala | missense_variant | 3/3 | 1 | NM_000482.4 | P1 | |
ENST00000645414.1 | n.169-61T>C | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.000962 AC: 146AN: 151754Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00125 AC: 313AN: 251308Hom.: 2 AF XY: 0.00142 AC XY: 193AN XY: 135836
GnomAD4 exome AF: 0.00128 AC: 1864AN: 1461854Hom.: 7 Cov.: 78 AF XY: 0.00137 AC XY: 993AN XY: 727224
GnomAD4 genome AF: 0.000942 AC: 143AN: 151874Hom.: 0 Cov.: 33 AF XY: 0.000889 AC XY: 66AN XY: 74210
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 22, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at