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Genomes
Filters Pass
Allele Count3
Allele Number152044
Allele Frequency0.00001973
Grpmax Filtering AF
(95% confidence)
0.00005290
Admixed American
Number of homozygotes1
Mean depth of coverage31.1

External Resources

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Genetic Ancestry Group Frequencies

31527010.0001965
06802800.000
01058600.000
091200.000
0518400.000
031600.000
04136400.000
0482400.000
0347200.000
0208800.000
XX17779400.00001285
XY27425010.00002694
Total315204410.00001973
Include:

Related 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.

  1. missense

    1. NSD2

      1. ENST00000508803.6
        MANE Select transcript for NSD2
        HGVSp
        p.Lys17Asn
        Domains
        • PTHR22884 (PANTHER)
        Polyphen
        benign
        SIFT
        tolerated_low_confidence
      2. ENST00000382895.7
        Ensembl canonical transcript for NSD2
        HGVSp
        p.Lys17Asn
        Domains
        • PTHR22884 (PANTHER)
        Polyphen
        benign
        SIFT
        tolerated_low_confidence
      3. ENST00000382891.9
        HGVSp
        p.Lys17Asn
        Domains
        • PTHR22884 (PANTHER)
        Polyphen
        benign
        SIFT
        tolerated_low_confidence
  2. non coding transcript exon

    1. NSD2

      1. ENST00000508355.5
        HGVSc
        n.169G>C

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.

ExpectedObservedConstraint
220.7176Z = 3.01
o/e = 0.8
Z Score not constrainedconstrained2.184.0

View the genomic constraint values for the 40kb region surrounding this variant: 4-1880705-1920705

ClinVar

ClinVar Variation ID
3202300
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
< 3030-3535-4040-4545-5050-5555-6060-6565-7070-7575-80> 80Age01Variant carriers05001.00K1.50K2.00K2.50K3.00K3.50K4.00K4.50KAll individuals

Genotype Quality Metrics

  • Exome
  • Genome
  • Variant carriers
  • All individuals
0-510-1520-2530-3540-4550-5560-6570-7580-8590-95> 100Genotype quality01Variant carriers02.00K4.00K6.00K8.00K10.0K12.0K14.0K16.0K18.0K20.0K22.0KAll individuals

Site Quality Metrics

  • Exome
  • Genome
1e11e1.51e21e2.51e31e3.51e41e4.51e51e5.51e61e6.51e71e7.51e81e8.51e91e9.51e10SiteQuality05.00M10.0M15.0M20.0M25.0M30.0MGenome variants2.009e+3

Value: 2.009e+3 (genome samples)

Site quality approximation for all variants with 0 <= AF < 0.00005.

Read Data


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