9-37422883-CGG-CG
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The ENST00000318158.11(GRHPR):c.83+52del 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 1,363,358 control chromosomes in the GnomAD database, including 21,753 homozygotes. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.15 ( 1901 hom., cov: 29)
Exomes 𝑓: 0.18 ( 19852 hom. )
Consequence
GRHPR
ENST00000318158.11 intron
ENST00000318158.11 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.433
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 -10 ACMG points.
BP6
Variant 9-37422883-CG-C is Benign according to our data. Variant chr9-37422883-CG-C is described in ClinVar as [Benign]. Clinvar id is 204218.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.183 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GRHPR | NM_012203.2 | c.83+52del | intron_variant | ENST00000318158.11 | NP_036335.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GRHPR | ENST00000318158.11 | c.83+52del | intron_variant | 1 | NM_012203.2 | ENSP00000313432 | P1 |
Frequencies
GnomAD3 genomes AF: 0.149 AC: 22613AN: 152074Hom.: 1899 Cov.: 29
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GnomAD3 exomes AF: 0.166 AC: 24285AN: 146674Hom.: 2265 AF XY: 0.165 AC XY: 13090AN XY: 79494
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GnomAD4 exome AF: 0.176 AC: 213228AN: 1211166Hom.: 19852 Cov.: 12 AF XY: 0.175 AC XY: 105998AN XY: 604794
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GnomAD4 genome AF: 0.149 AC: 22617AN: 152192Hom.: 1901 Cov.: 29 AF XY: 0.148 AC XY: 10991AN XY: 74396
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ClinVar
Significance: Benign
Submissions summary: Uncertain:1Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Primary hyperoxaluria, type II Uncertain:1Benign:1
Benign, criteria provided, single submitter | clinical testing | Mendelics | Jan 23, 2024 | - - |
Uncertain significance, no assertion criteria provided | research | Clinical Biochemistry Laboratory, Health Services Laboratory | Nov 27, 2014 | - - |
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at