Help us continue to improve gnomAD by taking 5 minutes to fill out our user survey.
SNV:4-1900705-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 | 3 |
| Allele Number | 152044 |
| Allele Frequency | 0.00001973 |
| Grpmax Filtering AF (95% confidence) | 0.00005290 Admixed American |
| Number of homozygotes | 1 |
| Mean depth of coverage | 31.1 |
External Resources
Feedback
Report an issue with this variantGenetic Ancestry Group Frequencies
- gnomAD
- HGDP
- 1KG
- Local Ancestry
| 3 | 15270 | 1 | 0.0001965 | ||
| 0 | 68028 | 0 | 0.000 | ||
| 0 | 10586 | 0 | 0.000 | ||
| 0 | 912 | 0 | 0.000 | ||
| 0 | 5184 | 0 | 0.000 | ||
| 0 | 316 | 0 | 0.000 | ||
| 0 | 41364 | 0 | 0.000 | ||
| 0 | 4824 | 0 | 0.000 | ||
| 0 | 3472 | 0 | 0.000 | ||
| 0 | 2088 | 0 | 0.000 | ||
| XX | 1 | 77794 | 0 | 0.00001285 | |
| XY | 2 | 74250 | 1 | 0.00002694 | |
| Total | 3 | 152044 | 1 | 0.00001973 | |
Include:
Related Variants
Nearby Variants
Variant Effect Predictor
This variant falls on 16 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
NSD2
- ENST00000508803.6MANE Select transcript for NSD2
- HGVSp
- p.Lys17Asn
- Domains
- PTHR22884 (PANTHER)
- Polyphen
- benign
- SIFT
- tolerated_low_confidence
- ENST00000382895.7Ensembl canonical transcript for NSD2
- HGVSp
- p.Lys17Asn
- Domains
- PTHR22884 (PANTHER)
- Polyphen
- benign
- SIFT
- tolerated_low_confidence
- ENST00000382891.9
- HGVSp
- p.Lys17Asn
- Domains
- PTHR22884 (PANTHER)
- Polyphen
- benign
- SIFT
- tolerated_low_confidence
- ENST00000508803.6
non coding transcript exon
NSD2
- ENST00000508355.5
- HGVSc
- n.169G>C
- ENST00000508355.5
In Silico Predictors
Transcript-specific predictors SIFT and Polyphen are listed with Variant Effect Predictor annotations.
- REVEL: 0.0810
- CADD: 17.4
- SpliceAI: 0.00 (no_consequence)
- PrimateAI: 0.366
Genomic Constraint of Surrounding 1kb Region
Genomic constraint values displayed are for the region: 4-1900000-1901000
Read more about this constraint.
| Expected | Observed | Constraint |
|---|---|---|
| 220.7 | 176 | Z = 3.01 o/e = 0.8 |
Z Score
View the genomic constraint values for the 40kb region surrounding this variant: 4-1880705-1920705
ClinVar
- ClinVar Variation ID
- 3202300
- Conditions
- Inborn genetic diseases
- Germline classification
- Uncertain significance
- Review status
- criteria provided, single submitter (1 star)
- Last evaluated
- June 21, 2021
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: 2.009e+3 (genome samples)
Site quality approximation for all variants with 0 <= AF < 0.00005.
Read Data
Always load read data