rs763846768
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 2P and 12B. PM2BP4_StrongBP6_Very_Strong
The ENST00000233242.5(APOB):āc.3971A>Cā(p.Lys1324Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000335 in 1,614,060 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. K1324N) has been classified as Uncertain significance.
Frequency
Consequence
ENST00000233242.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
APOB | NM_000384.3 | c.3971A>C | p.Lys1324Thr | missense_variant | 25/29 | ENST00000233242.5 | NP_000375.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
APOB | ENST00000233242.5 | c.3971A>C | p.Lys1324Thr | missense_variant | 25/29 | 1 | NM_000384.3 | ENSP00000233242 | P1 | |
APOB | ENST00000673739.2 | c.*3277A>C | 3_prime_UTR_variant, NMD_transcript_variant | 24/25 | ENSP00000501110 | |||||
APOB | ENST00000673882.2 | c.*3066A>C | 3_prime_UTR_variant, NMD_transcript_variant | 23/23 | ENSP00000501253 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152172Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000175 AC: 44AN: 251408Hom.: 0 AF XY: 0.000118 AC XY: 16AN XY: 135874
GnomAD4 exome AF: 0.0000342 AC: 50AN: 1461888Hom.: 0 Cov.: 33 AF XY: 0.0000261 AC XY: 19AN XY: 727244
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152172Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74346
ClinVar
Submissions by phenotype
Hypercholesterolemia, autosomal dominant, type B;C4551990:Familial hypobetalipoproteinemia 1 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Oct 06, 2023 | - - |
Cardiovascular phenotype Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 16, 2023 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at