rs61746672
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_000384.3(APOB):c.606A>T(p.Glu202Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000742 in 1,614,204 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_000384.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
APOB | NM_000384.3 | c.606A>T | p.Glu202Asp | missense_variant | 6/29 | ENST00000233242.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
APOB | ENST00000233242.5 | c.606A>T | p.Glu202Asp | missense_variant | 6/29 | 1 | NM_000384.3 | P1 | |
APOB | ENST00000399256.4 | c.606A>T | p.Glu202Asp | missense_variant | 6/17 | 1 | |||
APOB | ENST00000673739.2 | c.452A>T | p.Lys151Ile | missense_variant, NMD_transcript_variant | 5/25 | ||||
APOB | ENST00000673882.2 | c.452A>T | p.Lys151Ile | missense_variant, NMD_transcript_variant | 5/23 |
Frequencies
GnomAD3 genomes ? AF: 0.00354 AC: 539AN: 152196Hom.: 4 Cov.: 32
GnomAD3 exomes AF: 0.00112 AC: 282AN: 251446Hom.: 2 AF XY: 0.000839 AC XY: 114AN XY: 135896
GnomAD4 exome AF: 0.000451 AC: 659AN: 1461890Hom.: 5 Cov.: 32 AF XY: 0.000378 AC XY: 275AN XY: 727246
GnomAD4 genome ? AF: 0.00354 AC: 539AN: 152314Hom.: 4 Cov.: 32 AF XY: 0.00332 AC XY: 247AN XY: 74480
ClinVar
Submissions by phenotype
not provided Benign:5
Likely benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Feb 11, 2016 | - - |
Likely benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Oct 13, 2023 | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jun 01, 2022 | APOB: BP4 - |
Benign, criteria provided, single submitter | clinical testing | Quest Diagnostics Nichols Institute San Juan Capistrano | Jun 13, 2020 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 13, 2020 | - - |
Familial hypercholesterolemia Benign:2
Benign, criteria provided, single submitter | clinical testing | Color Diagnostics, LLC DBA Color Health | Jun 28, 2018 | - - |
Benign, criteria provided, single submitter | clinical testing | GENinCode PLC | Jun 23, 2022 | - - |
Hypercholesterolemia, autosomal dominant, type B;C4551990:Familial hypobetalipoproteinemia 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Hypercholesterolemia, familial, 1 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Robarts Research Institute, Western University | Jan 02, 2018 | - - |
Cardiovascular phenotype Benign:1
Benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 07, 2017 | This alteration is classified as 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