9-37436635-CCTCTCTCTCTCT-CCTCTCT

Variant names:

• chr9-37436635-CCTCTCT-C
• rs34302950
• NM_012203.2:c.866-14_866-9delTCTCTC

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BS1 BS2

The NM_012203.2(GRHPR):​c.866-14_866-9delTCTCTC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00118 in 1,525,216 control chromosomes in the GnomAD database, including 7 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.0053 (4 hom., cov: 28)
  • Exomes 𝑓: 0.00073 (3 hom.)
• Consequence: GRHPR NM_012203.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.455

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 Benign. Variant got -10 ACMG points.

• BP6: Variant 9-37436635-CCTCTCT-C is Benign according to our data. Variant chr9-37436635-CCTCTCT-C is described in ClinVar as [Benign]. Clinvar id is 1572176.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00531 (803/151142) while in subpopulation AFR AF= 0.0177 (731/41266). AF 95% confidence interval is 0.0166. There are 4 homozygotes in gnomad4. There are 382 alleles in male gnomad4 subpopulation. Median coverage is 28. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 4 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GRHPR	NM_012203.2	c.866-14_866-9delTCTCTC		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_866-20delCTCTCT		intron_variant	Intron 8 of 8	1	NM_012203.2	ENSP00000313432.6

Frequencies

GnomAD3 genomes AF: 0.00528 AC: 798 AN: 151036 Hom.: 4 Cov.: 28

Gnomad AFR AF: 0.0176

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00277

Gnomad ASJ AF: 0.00116

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.000209

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00318

Gnomad NFE AF: 0.000251

Gnomad OTH AF: 0.00242

GnomAD4 exome AF: 0.000728 AC: 1000 AN: 1374074 Hom.: 3 AF XY: 0.000649 AC XY: 444 AN XY: 684078

Gnomad4 AFR exome AF: 0.0183

Gnomad4 AMR exome AF: 0.00186

Gnomad4 ASJ exome AF: 0.00235

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000123

Gnomad4 FIN exome AF: 0.0000199

Gnomad4 NFE exome AF: 0.000172

Gnomad4 OTH exome AF: 0.00160

GnomAD4 genome AF: 0.00531 AC: 803 AN: 151142 Hom.: 4 Cov.: 28 AF XY: 0.00518 AC XY: 382 AN XY: 73810

Gnomad4 AFR AF: 0.0177

Gnomad4 AMR AF: 0.00276

Gnomad4 ASJ AF: 0.00116

Gnomad4 EAS AF: 0.000387

Gnomad4 SAS AF: 0.000209

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000251

Gnomad4 OTH AF: 0.00239

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Dec 13, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs34302950; hg19: chr9-37436632;