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rs34302950

chr9-37436635-CCTCTCTCTCT-Cchr9-37436635-CCTCTCTCTCT-CCTchr9-37436635-CCTCTCTCTCT-CCTCTchr9-37436635-CCTCTCTCTCT-CCTCTCTchr9-37436635-CCTCTCTCTCT-CCTCTCTCTchr9-37436635-CCTCTCTCTCT-CCTCTCTCTCTCTchr9-37436635-CCTCTCTCTCT-CCTCTCTCTCTCTCTchr9-37436635-CCTCTCTCTCT-CCTCTCTCTCTCTCTCTchr9-37436635-CCTCTCTCTCT-CCTCTCTCTCTCTCTCTCTCTCTCTchr9-37436635-CCTCTCTCTCT-CCTCTCTCTCTCTCTCTCTCTCTCTCT

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP6_Moderate

The NM_012203.2(GRHPR):c.866-18_866-9del variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000218 in 1,374,128 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: not found (cov: 28)
Exomes 𝑓: 0.0000022 ( 0 hom. )

Consequence

GRHPR
NM_012203.2 splice_polypyrimidine_tract, intron

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.668
Variant links:
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 Uncertain_significance. Variant got 0 ACMG points.

PM2
?
    PM2 - Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
Very rare variant in population databases, with high coverage;
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 9-37436635-CCTCTCTCTCT-C is Benign according to our data. Variant chr9-37436635-CCTCTCTCTCT-C is described in ClinVar as [Likely_benign]. Clinvar id is 2899870.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
GRHPRNM_012203.2 linkuse as main transcriptc.866-18_866-9del splice_polypyrimidine_tract_variant, intron_variant ENST00000318158.11

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
GRHPRENST00000318158.11 linkuse as main transcriptc.866-18_866-9del splice_polypyrimidine_tract_variant, intron_variant 1 NM_012203.2 P1Q9UBQ7-1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
Cov.:
28
GnomAD4 exome
AF:
0.00000218
AC:
3
AN:
1374128
Hom.:
0
AF XY:
0.00000292
AC XY:
2
AN XY:
684104
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000287
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
Cov.:
28
Bravo
AF:
0.0000113

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Likely benign, criteria provided, single submitterclinical testingInvitaeJan 31, 2024- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs34302950; hg19: chr9-37436632; API