rs34302950

Variant names:

• chr9-37436635-CCTCTCTCTCTCT-C
• NM_012203.2:c.866-20_866-9delTCTCTCTCTCTC

Your query was ambiguous. Multiple possible variants found:

• chr9-37436635-CCTCTCTCTCTCT-C
• chr9-37436635-CCTCTCTCTCTCT-CCT
• chr9-37436635-CCTCTCTCTCTCT-CCTCT
• chr9-37436635-CCTCTCTCTCTCT-CCTCTCT
• chr9-37436635-CCTCTCTCTCTCT-CCTCTCTCT
• chr9-37436635-CCTCTCTCTCTCT-CCTCTCTCTCT
• chr9-37436635-CCTCTCTCTCTCT-CCTCTCTCTCTCTCT
• chr9-37436635-CCTCTCTCTCTCT-CCTCTCTCTCTCTCTCT
• chr9-37436635-CCTCTCTCTCTCT-CCTCTCTCTCTCTCTCTCT
• chr9-37436635-CCTCTCTCTCTCT-CCTCTCTCTCTCTCTCTCTCTCTCTCT
• chr9-37436635-CCTCTCTCTCTCT-CCTCTCTCTCTCTCTCTCTCTCTCTCTCT

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_012203.2(GRHPR):​c.866-20_866-9delTCTCTCTCTCTC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000728 in 1,374,128 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 28)
  • Exomes 𝑓: 7.3e-7 (0 hom.)
• Consequence: GRHPR NM_012203.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.668

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GRHPR	NM_012203.2	c.866-20_866-9delTCTCTCTCTCTC		intron_variant	Intron 8 of 8	ENST00000318158.11	NP_036335.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GRHPR	ENST00000318158.11	c.866-25_866-14delCTCTCTCTCTCT		intron_variant	Intron 8 of 8	1	NM_012203.2	ENSP00000313432.6

Frequencies

GnomAD3 genomes Cov.: 28

GnomAD4 exome AF: 7.28e-7 AC: 1 AN: 1374128 Hom.: 0 AF XY: 0.00000146 AC XY: 1 AN XY: 684104

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: 9.56e-7

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 28

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr9-37436632;