rs75307540
Positions:
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_000613.3(HPX):c.1111C>T(p.Arg371Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000753 in 1,613,944 control chromosomes in the GnomAD database, including 12 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0040 ( 6 hom., cov: 32)
Exomes 𝑓: 0.00042 ( 6 hom. )
Consequence
HPX
NM_000613.3 missense
NM_000613.3 missense
Scores
4
14
Clinical Significance
Conservation
PhyloP100: 0.932
Genes affected
HPX (HGNC:5171): (hemopexin) This gene encodes a plasma glycoprotein that binds heme with high affinity. The encoded protein is an acute phase protein that transports heme from the plasma to the liver and may be involved in protecting cells from oxidative stress. [provided by RefSeq, Apr 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.010905713).
BP6
?
Variant 11-6431659-G-A is Benign according to our data. Variant chr11-6431659-G-A is described in ClinVar as [Benign]. Clinvar id is 784185.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High Homozygotes in GnomAd4 at 6 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HPX | NM_000613.3 | c.1111C>T | p.Arg371Trp | missense_variant | 9/10 | ENST00000265983.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HPX | ENST00000265983.8 | c.1111C>T | p.Arg371Trp | missense_variant | 9/10 | 1 | NM_000613.3 | P1 | |
HPX | ENST00000527556.5 | n.939C>T | non_coding_transcript_exon_variant | 3/4 | 2 | ||||
HPX | ENST00000529037.1 | n.578C>T | non_coding_transcript_exon_variant | 2/3 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00400 AC: 608AN: 152174Hom.: 6 Cov.: 32
GnomAD3 genomes
?
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GnomAD3 exomes AF: 0.00101 AC: 254AN: 250886Hom.: 2 AF XY: 0.000767 AC XY: 104AN XY: 135552
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GnomAD4 exome AF: 0.000417 AC: 609AN: 1461652Hom.: 6 Cov.: 32 AF XY: 0.000367 AC XY: 267AN XY: 727128
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GnomAD4 genome ? AF: 0.00399 AC: 607AN: 152292Hom.: 6 Cov.: 32 AF XY: 0.00379 AC XY: 282AN XY: 74466
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Mar 02, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
D
LIST_S2
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M
MutationTaster
Benign
N
PrimateAI
Benign
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Uncertain
D
Sift4G
Uncertain
D
Polyphen
D
Vest4
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
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