16-72055841-A-G
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_005143.5(HP):c.6-320A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.554 in 384,938 control chromosomes in the GnomAD database, including 60,709 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 0.56 ( 23944 hom., cov: 30)
Exomes 𝑓: 0.55 ( 36765 hom. )
Consequence
HP
NM_005143.5 intron
NM_005143.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.08
Genes affected
HP (HGNC:5141): (haptoglobin) This gene encodes a preproprotein, which is processed to yield both alpha and beta chains, which subsequently combine as a tetramer to produce haptoglobin. Haptoglobin functions to bind free plasma hemoglobin, which allows degradative enzymes to gain access to the hemoglobin, while at the same time preventing loss of iron through the kidneys and protecting the kidneys from damage by hemoglobin. Mutations in this gene and/or its regulatory regions cause ahaptoglobinemia or hypohaptoglobinemia. This gene has also been linked to diabetic nephropathy, the incidence of coronary artery disease in type 1 diabetes, Crohn's disease, inflammatory disease behavior, primary sclerosing cholangitis, susceptibility to idiopathic Parkinson's disease, and a reduced incidence of Plasmodium falciparum malaria. The protein encoded also exhibits antimicrobial activity against bacteria. A similar duplicated gene is located next to this gene on chromosome 16. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2014]
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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=-0.9).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.632 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HP | NM_005143.5 | c.6-320A>G | intron_variant | ENST00000355906.10 | NP_005134.1 | |||
HP | NM_001126102.3 | c.6-320A>G | intron_variant | NP_001119574.1 | ||||
HP | NM_001318138.2 | c.6-320A>G | intron_variant | NP_001305067.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HP | ENST00000355906.10 | c.6-320A>G | intron_variant | 1 | NM_005143.5 | ENSP00000348170 | A2 |
Frequencies
GnomAD3 genomes AF: 0.557 AC: 84429AN: 151608Hom.: 23921 Cov.: 30
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GnomAD4 exome AF: 0.553 AC: 128913AN: 233210Hom.: 36765 Cov.: 3 AF XY: 0.563 AC XY: 71549AN XY: 127148
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GnomAD4 genome AF: 0.557 AC: 84497AN: 151728Hom.: 23944 Cov.: 30 AF XY: 0.556 AC XY: 41215AN XY: 74096
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ClinVar
Not reported inComputational scores
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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