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SNV:10-97584911-C-T (GRCh38)
Dataset
- gnomAD v3.1.2
- GRCh38
- gnomAD v4.1.0807,162 samples
- gnomAD v4.1.0 (non-UKB)314,392 samples
- gnomAD v3.1.276,156 samples
- gnomAD v3.1.2 (non-cancer)74,023 samples
- gnomAD v3.1.2 (non-neuro)67,442 samples
- gnomAD v3.1.2 (non-v2)57,344 samples
- gnomAD v3.1.2 (non-TOPMed)40,433 samples
- gnomAD v3.1.2 (controls/biobanks)16,465 samples
- GRCh37
- gnomAD v2.1.1141,456 samples
- gnomAD v2.1.1 (non-TOPMed)135,743 samples
- gnomAD v2.1.1 (non-cancer)134,187 samples
- gnomAD v2.1.1 (non-neuro)114,704 samples
- gnomAD v2.1.1 (controls)60,146 samples
| Genomes | |
|---|---|
| Filters | Pass |
| Allele Count | 3 |
| Allele Number | 152144 |
| Allele Frequency | 0.00001972 |
| Grpmax Filtering AF (95% confidence) | 0.00001171 European (non-Finnish) |
| Number of homozygotes | 0 |
| Mean depth of coverage | 31.5 |
External Resources
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Report an issue with this variantGenetic Ancestry Group Frequencies
- gnomAD
- HGDP
- 1KG
- Local Ancestry
| 3 | 68036 | 0 | 0.00004409 | ||
| 0 | 10620 | 0 | 0.000 | ||
| 0 | 15270 | 0 | 0.000 | ||
| 0 | 912 | 0 | 0.000 | ||
| 0 | 5182 | 0 | 0.000 | ||
| 0 | 316 | 0 | 0.000 | ||
| 0 | 41428 | 0 | 0.000 | ||
| 0 | 4822 | 0 | 0.000 | ||
| 0 | 3468 | 0 | 0.000 | ||
| 0 | 2090 | 0 | 0.000 | ||
| XX | 2 | 77830 | 0 | 0.00002570 | |
| XY | 1 | 74314 | 0 | 0.00001346 | |
| Total | 3 | 152144 | 0 | 0.00001972 | |
Include:
Related Variants
Nearby Variants
Ensembl Variant Effect Predictor
This variant falls on 4 transcripts in 2 genes.
Note The gene symbols shown below are provided by VEP and may differ from the symbol shown on gene pages.
stop gained
HOGA1
- ENST00000370646.9MANE Select transcript for HOGA1
- HGVSp
- p.Arg70Ter
- Domains
- pLoF
- High-confidence
- ENST00000370647.8
- HGVSp
- p.Arg70Ter
- Domains
- cd00408 (CDD)
- pLoF
- High-confidence
- ENST00000370646.9
AL355315.1
- ENST00000370649.3Ensembl canonical transcript for AL355315.1
- HGVSp
- p.Arg70Ter
- Domains
- 3 (Gene3D)
- pLoF
- High-confidence
- ENST00000370649.3
non coding transcript exon
HOGA1
- ENST00000465608.1
- HGVSc
- n.589C>T
- ENST00000465608.1
In Silico Predictors
Transcript-specific predictors SIFT and Polyphen are listed with Variant Effect Predictor annotations.
- CADD: 36.0
- SpliceAI: 0.0100 (donor_loss)
Note This variant has multiple SpliceAI scores
Genomic Constraint of Surrounding 1kb Region
Genomic constraint values displayed are for the region: 10-97584000-97585000
Read more about this constraint.
| Expected | Observed | Constraint |
|---|---|---|
| 214.1 | 195 | Z = 1.31 o/e = 0.91 |
Z Score
View the genomic constraint values for the 40kb region surrounding this variant: 10-97564911-97604911
ClinVar
- ClinVar Variation ID
- 204269
- Conditions
- Primary hyperoxaluria type 3, not provided
- Germline classification
- Pathogenic
- Review status
- criteria provided, multiple submitters, no conflicts (2 stars)
- Last evaluated
- September 5, 2024
or find more information on the ClinVar website. Data displayed here is from ClinVar's February 1, 2025 release.
Age Distribution
- Exome
- Genome
- Variant carriers
- All individuals
Genotype Quality Metrics
- Genotype quality
- Depth
- Allele balance for heterozygotes
- Exome
- Genome
- Variant carriers
- All individuals
Site Quality Metrics
- Metric distribution
- All metric values
- Exome
- Genome
Value: 5.075e+3 (genome samples)
Site quality approximation for all variants with 0 <= AF < 0.00005.
Read Data
Always load read data