rs2000999
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_020995.4(HPR):c.92-90G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.206 in 1,287,932 control chromosomes in the GnomAD database, including 31,177 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 ( 2784 hom., cov: 32)
Exomes 𝑓: 0.21 ( 28393 hom. )
Consequence
HPR
NM_020995.4 intron
NM_020995.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.138
Genes affected
HPR (HGNC:5156): (haptoglobin-related protein) This gene encodes a haptoglobin-related protein that binds hemoglobin as efficiently as haptoglobin. Unlike haptoglobin, plasma concentration of this protein is unaffected in patients with sickle cell anemia and extensive intravascular hemolysis, suggesting a difference in binding between haptoglobin-hemoglobin and haptoglobin-related protein-hemoglobin complexes to CD163, the hemoglobin scavenger receptor. This protein may also be a clinically important predictor of recurrence of breast cancer. [provided by RefSeq, Oct 2011]
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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=-0.86).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.38 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HPR | NM_020995.4 | c.92-90G>A | intron_variant | ENST00000540303.7 | |||
HPR | NM_001384360.1 | c.-269-90G>A | intron_variant | ||||
HPR | XM_024450251.2 | c.110-90G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HPR | ENST00000540303.7 | c.92-90G>A | intron_variant | 1 | NM_020995.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.170 AC: 25742AN: 151344Hom.: 2786 Cov.: 32
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GnomAD4 exome AF: 0.211 AC: 239835AN: 1136468Hom.: 28393 AF XY: 0.219 AC XY: 127456AN XY: 580740
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GnomAD4 genome ? AF: 0.170 AC: 25736AN: 151464Hom.: 2784 Cov.: 32 AF XY: 0.174 AC XY: 12869AN XY: 74030
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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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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at