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SNV:19-12940316-G-C (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 | 131 |
| Allele Number | 152200 |
| Allele Frequency | 0.0008607 |
| Grpmax Filtering AF (95% confidence) | 0.001345 European (non-Finnish) |
| Number of homozygotes | 0 |
| Mean depth of coverage | 31.1 |
External Resources
Feedback
Report an issue with this variantGenetic Ancestry Group Frequencies
- gnomAD
- HGDP
- 1KG
- Local Ancestry
| 108 | 68046 | 0 | 0.001587 | ||
| 2 | 2092 | 0 | 0.0009560 | ||
| 17 | 41446 | 0 | 0.0004102 | ||
| 4 | 15270 | 0 | 0.0002620 | ||
| 0 | 10618 | 0 | 0.000 | ||
| 0 | 912 | 0 | 0.000 | ||
| 0 | 5198 | 0 | 0.000 | ||
| 0 | 316 | 0 | 0.000 | ||
| 0 | 4830 | 0 | 0.000 | ||
| 0 | 3472 | 0 | 0.000 | ||
| XX | 80 | 77846 | 0 | 0.001028 | |
| XY | 51 | 74354 | 0 | 0.0006859 | |
| Total | 131 | 152200 | 0 | 0.0008607 | |
Include:
Related Variants
Nearby Variants
Variant Effect Predictor
This variant falls on 3 transcripts in 1 gene.
Note The gene symbols shown below are provided by VEP and may differ from the symbol shown on gene pages.
missense
CALR
- ENST00000316448.10MANE Select transcript for CALR
- HGVSp
- p.Ser189Thr
- Domains
- Polyphen
- benign
- SIFT
- tolerated
- ENST00000588454.5
- HGVSp
- p.Ser121Thr
- Domains
- Polyphen
- benign
- SIFT
- deleterious
- ENST00000316448.10
non coding transcript exon
CALR
- ENST00000590325.1
- HGVSc
- n.727G>C
- ENST00000590325.1
In Silico Predictors
Transcript-specific predictors SIFT and Polyphen are listed with Variant Effect Predictor annotations.
- REVEL: 0.0360
- CADD: 22.3
- SpliceAI: 0.0300 (acceptor_gain)
- PrimateAI: 0.458
Genomic Constraint of Surrounding 1kb Region
Genomic constraint values displayed are for the region: 19-12940000-12941000
Read more about this constraint.
| Expected | Observed | Constraint |
|---|---|---|
| 240.5 | 221 | Z = 1.26 o/e = 0.92 |
Z Score
View the genomic constraint values for the 40kb region surrounding this variant: 19-12920316-12960316
ClinVar
- ClinVar Variation ID
- 3046043
- Conditions
- CALR-related disorder
- Germline classification
- Likely benign
- Review status
- no assertion criteria provided (0 stars)
- Last evaluated
- February 1, 2022
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: 1.437e+5 (genome samples)
Site quality approximation for all variants with 0.0005 <= AF < 0.001.
Read Data
Always load read data