rs137853233
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP4BP6
The NM_005143.5(HP):c.214A>G(p.Lys72Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 14/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Genomes: not found (cov: 19)
Consequence
HP
NM_005143.5 missense
NM_005143.5 missense
Scores
2
2
14
Clinical Significance
Conservation
PhyloP100: 2.37
Publications
3 publications found
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 was made for transcript
Our verdict: Likely_benign. The variant received -2 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.2689277).
BP6
Variant 16-72057415-A-G is Benign according to our data. Variant chr16-72057415-A-G is described in ClinVar as Benign. ClinVar VariationId is 15898.Status of the report is no_assertion_criteria_provided, 0 stars.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_005143.5. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| HP | TSL:1 MANE Select | c.214A>G | p.Lys72Glu | missense | Exon 4 of 7 | ENSP00000348170.5 | P00738-1 | ||
| HP | TSL:1 | c.214A>G | p.Lys72Glu | missense | Exon 4 of 5 | ENSP00000454966.1 | A0A0C4DGL8 | ||
| HP | TSL:1 | c.190+784A>G | intron | N/A | ENSP00000381199.2 | P00738-2 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
19
GnomAD4 exome Cov.: 14
GnomAD4 exome
Cov.:
14
GnomAD4 genome
GnomAD4 genome
Cov.:
19
ClinVar
ClinVar submissions
View on ClinVar Significance:Benign
Revision:no assertion criteria provided
Pathogenic
VUS
Benign
Condition
-
-
1
HAPTOGLOBIN, ALPHA-1, FAST-SLOW POLYMORPHISM (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
DANN
Benign
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
D
LIST_S2
Uncertain
D
M_CAP
Benign
D
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Pathogenic
M
PhyloP100
PrimateAI
Uncertain
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Pathogenic
D
Polyphen
D
Vest4
MutPred
Loss of ubiquitination at K72 (P = 0.0244)
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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