rs1544556
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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.982+43C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.217 in 1,542,258 control chromosomes in the GnomAD database, including 40,866 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 0.17 ( 2790 hom., cov: 32)
Exomes 𝑓: 0.22 ( 38076 hom. )
Consequence
APOH
NM_000042.3 intron
NM_000042.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.206
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=-0.83).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.252 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
APOH | NM_000042.3 | c.982+43C>T | intron_variant | ENST00000205948.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
APOH | ENST00000205948.11 | c.982+43C>T | intron_variant | 1 | NM_000042.3 | P1 | |||
APOH | ENST00000585162.1 | c.258-2222C>T | intron_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.166 AC: 25232AN: 151830Hom.: 2790 Cov.: 32
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GnomAD3 exomes AF: 0.167 AC: 41269AN: 247214Hom.: 4407 AF XY: 0.167 AC XY: 22355AN XY: 133778
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GnomAD4 exome AF: 0.222 AC: 308884AN: 1390310Hom.: 38076 Cov.: 22 AF XY: 0.218 AC XY: 151515AN XY: 696048
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GnomAD4 genome ? AF: 0.166 AC: 25234AN: 151948Hom.: 2790 Cov.: 32 AF XY: 0.160 AC XY: 11846AN XY: 74262
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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
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