9-37422883-CGG-CG

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

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter U:1B:1

Conservation

PhyloP100: -0.433
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]

Genome browser will be placed here

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
GRHPRNM_012203.2 linkuse as main transcriptc.83+52del intron_variant ENST00000318158.11 NP_036335.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
GRHPRENST00000318158.11 linkuse as main transcriptc.83+52del intron_variant 1 NM_012203.2 ENSP00000313432 P1Q9UBQ7-1

Frequencies

GnomAD3 genomes
AF:
0.149
AC:
22613
AN:
152074
Hom.:
1899
Cov.:
29
show subpopulations
Gnomad AFR
AF:
0.0755
Gnomad AMI
AF:
0.256
Gnomad AMR
AF:
0.182
Gnomad ASJ
AF:
0.252
Gnomad EAS
AF:
0.0431
Gnomad SAS
AF:
0.129
Gnomad FIN
AF:
0.158
Gnomad MID
AF:
0.250
Gnomad NFE
AF:
0.186
Gnomad OTH
AF:
0.172
GnomAD3 exomes
AF:
0.166
AC:
24285
AN:
146674
Hom.:
2265
AF XY:
0.165
AC XY:
13090
AN XY:
79494
show subpopulations
Gnomad AFR exome
AF:
0.0742
Gnomad AMR exome
AF:
0.193
Gnomad ASJ exome
AF:
0.246
Gnomad EAS exome
AF:
0.0394
Gnomad SAS exome
AF:
0.132
Gnomad FIN exome
AF:
0.153
Gnomad NFE exome
AF:
0.194
Gnomad OTH exome
AF:
0.181
GnomAD4 exome
AF:
0.176
AC:
213228
AN:
1211166
Hom.:
19852
Cov.:
12
AF XY:
0.175
AC XY:
105998
AN XY:
604794
show subpopulations
Gnomad4 AFR exome
AF:
0.0719
Gnomad4 AMR exome
AF:
0.188
Gnomad4 ASJ exome
AF:
0.246
Gnomad4 EAS exome
AF:
0.0304
Gnomad4 SAS exome
AF:
0.131
Gnomad4 FIN exome
AF:
0.159
Gnomad4 NFE exome
AF:
0.187
Gnomad4 OTH exome
AF:
0.174
GnomAD4 genome
AF:
0.149
AC:
22617
AN:
152192
Hom.:
1901
Cov.:
29
AF XY:
0.148
AC XY:
10991
AN XY:
74396
show subpopulations
Gnomad4 AFR
AF:
0.0753
Gnomad4 AMR
AF:
0.183
Gnomad4 ASJ
AF:
0.252
Gnomad4 EAS
AF:
0.0428
Gnomad4 SAS
AF:
0.129
Gnomad4 FIN
AF:
0.158
Gnomad4 NFE
AF:
0.186
Gnomad4 OTH
AF:
0.170
Alfa
AF:
0.176
Hom.:
460
Bravo
AF:
0.149
Asia WGS
AF:
0.0960
AC:
337
AN:
3478

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 submitterclinical testingMendelicsJan 23, 2024- -
Uncertain significance, no assertion criteria providedresearchClinical Biochemistry Laboratory, Health Services LaboratoryNov 27, 2014- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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: rs35891798; hg19: chr9-37422880; API