9-37436635-CCTCTCTCTCT-CCTCTCTCTCTCT
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Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1
The NM_012203.2(GRHPR):c.866-10_866-9dup variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.173 in 1,516,950 control chromosomes in the GnomAD database, including 7,536 homozygotes. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.15 ( 1896 hom., cov: 28)
Exomes 𝑓: 0.18 ( 5640 hom. )
Consequence
GRHPR
NM_012203.2 intron
NM_012203.2 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.689
Genes affected
GRHPR (HGNC:4570): (glyoxylate and hydroxypyruvate reductase) This gene encodes an enzyme with hydroxypyruvate reductase, glyoxylate reductase, and D-glycerate dehydrogenase enzymatic activities. The enzyme has widespread tissue expression and has a role in metabolism. Type II hyperoxaluria is caused by mutations in this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -16 ACMG points.
BP6
Variant 9-37436635-C-CCT is Benign according to our data. Variant chr9-37436635-C-CCT is described in ClinVar as [Benign]. Clinvar id is 204227.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.189 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GRHPR | NM_012203.2 | c.866-10_866-9dup | intron_variant | ENST00000318158.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GRHPR | ENST00000318158.11 | c.866-10_866-9dup | intron_variant | 1 | NM_012203.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.151 AC: 22868AN: 150990Hom.: 1895 Cov.: 28
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GnomAD4 exome AF: 0.175 AC: 239486AN: 1365854Hom.: 5640 Cov.: 29 AF XY: 0.175 AC XY: 118973AN XY: 680316
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GnomAD4 genome AF: 0.151 AC: 22884AN: 151096Hom.: 1896 Cov.: 28 AF XY: 0.149 AC XY: 10996AN XY: 73784
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ClinVar
Significance: Benign
Submissions summary: Uncertain:1Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Primary hyperoxaluria, type II Uncertain:1Benign:1
Uncertain significance, no assertion criteria provided | research | Clinical Biochemistry Laboratory, Health Services Laboratory | Nov 27, 2014 | - - |
Benign, no assertion criteria provided | curation | GeneReviews | May 05, 2011 | - - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 02, 2020 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Computational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at