rs6933
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_000042.3(APOH):c.*21C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.587 in 1,595,720 control chromosomes in the GnomAD database, including 283,535 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.65 ( 33707 hom., cov: 33)
Exomes 𝑓: 0.58 ( 249828 hom. )
Consequence
APOH
NM_000042.3 3_prime_UTR
NM_000042.3 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.570
Genes affected
APOH (HGNC:616): (apolipoprotein H) Apolipoprotein H, also known as beta-2-glycoprotein I, is a component of circulating plasma lipoproteins. It has been implicated in a variety of physiologic pathways including lipoprotein metabolism, coagulation, hemostasis, and the production of antiphospholipid autoantibodies. APOH may be a required cofactor for anionic phospholipid binding by the antiphospholipid autoantibodies found in sera of many patients with lupus and primary antiphospholipid syndrome (APS). The anti-beta (2) glycoprotein I antibodies from APS patients, mediate inhibition of activated protein C which has anticoagulant properties. Because beta-2-GPI is the main autoantigen in patients with APS, the disruption of this pathway by autoantibodies may be an important mechanism for thrombosis in patients with APS.[provided by RefSeq, Dec 2019]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.907 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
APOH | NM_000042.3 | c.*21C>T | 3_prime_UTR_variant | 8/8 | ENST00000205948.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
APOH | ENST00000205948.11 | c.*21C>T | 3_prime_UTR_variant | 8/8 | 1 | NM_000042.3 | P1 | ||
APOH | ENST00000585162.1 | c.*21C>T | 3_prime_UTR_variant | 3/3 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.652 AC: 99054AN: 151988Hom.: 33640 Cov.: 33
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GnomAD3 exomes AF: 0.626 AC: 156499AN: 250168Hom.: 50937 AF XY: 0.616 AC XY: 83251AN XY: 135172
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GnomAD4 exome AF: 0.580 AC: 837844AN: 1443614Hom.: 249828 Cov.: 27 AF XY: 0.581 AC XY: 417863AN XY: 718936
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GnomAD4 genome ? AF: 0.652 AC: 99185AN: 152106Hom.: 33707 Cov.: 33 AF XY: 0.653 AC XY: 48523AN XY: 74338
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at