2-21016515-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 2P and 12B. PM2BP4_StrongBP6_Very_Strong
The NM_000384.3(APOB):c.3256G>A(p.Gly1086Ser) variant causes a missense change. The variant allele was found at a frequency of 0.000077 in 1,610,672 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt. Synonymous variant affecting the same amino acid position (i.e. G1086G) has been classified as Likely benign.
Frequency
Consequence
NM_000384.3 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 | UniProt |
---|---|---|---|---|---|---|---|
APOB | NM_000384.3 | c.3256G>A | p.Gly1086Ser | missense_variant | 21/29 | ENST00000233242.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
APOB | ENST00000233242.5 | c.3256G>A | p.Gly1086Ser | missense_variant | 21/29 | 1 | NM_000384.3 | P1 | |
APOB | ENST00000673739.2 | c.*2562G>A | 3_prime_UTR_variant, NMD_transcript_variant | 20/25 | |||||
APOB | ENST00000673882.2 | c.*2428-970G>A | intron_variant, NMD_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.000342 AC: 52AN: 152078Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000795 AC: 20AN: 251454Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135902
GnomAD4 exome AF: 0.0000494 AC: 72AN: 1458476Hom.: 0 Cov.: 29 AF XY: 0.0000482 AC XY: 35AN XY: 725832
GnomAD4 genome ? AF: 0.000342 AC: 52AN: 152196Hom.: 0 Cov.: 32 AF XY: 0.000282 AC XY: 21AN XY: 74420
ClinVar
Submissions by phenotype
Hypercholesterolemia, autosomal dominant, type B;C4551990:Familial hypobetalipoproteinemia 1 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Cardiovascular phenotype Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 06, 2021 | 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