rs13306190
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate
The NM_000384.3(APOB):c.1298C>T(p.Ala433Val) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000793 in 1,614,004 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. A433A) has been classified as Likely benign.
Frequency
Consequence
NM_000384.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
APOB | NM_000384.3 | c.1298C>T | p.Ala433Val | missense_variant | 10/29 | ENST00000233242.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
APOB | ENST00000233242.5 | c.1298C>T | p.Ala433Val | missense_variant | 10/29 | 1 | NM_000384.3 | P1 | |
APOB | ENST00000399256.4 | c.1298C>T | p.Ala433Val | missense_variant | 10/17 | 1 | |||
APOB | ENST00000673739.2 | c.*604C>T | 3_prime_UTR_variant, NMD_transcript_variant | 9/25 | |||||
APOB | ENST00000673882.2 | c.*604C>T | 3_prime_UTR_variant, NMD_transcript_variant | 9/23 |
Frequencies
GnomAD3 genomes ? AF: 0.000138 AC: 21AN: 152186Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000171 AC: 43AN: 251154Hom.: 0 AF XY: 0.000169 AC XY: 23AN XY: 135748
GnomAD4 exome AF: 0.0000732 AC: 107AN: 1461700Hom.: 0 Cov.: 31 AF XY: 0.0000743 AC XY: 54AN XY: 727138
GnomAD4 genome ? AF: 0.000138 AC: 21AN: 152304Hom.: 0 Cov.: 33 AF XY: 0.000134 AC XY: 10AN XY: 74468
ClinVar
Submissions by phenotype
Hypercholesterolemia, autosomal dominant, type B;C4551990:Familial hypobetalipoproteinemia 1 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 01, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at