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ExomesGenomesTotal
Filters No variantPass
Allele Count33
Allele Number152044152044
Allele Frequency0.000019730.00001973
Grpmax Filtering AF
(95% confidence)
0.00005290
Admixed American
Number of homozygotes11
Mean depth of coverage31.1

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Genetic Ancestry Group Frequencies

31527010.0001965
06802800.000
04136400.000
0347200.000
0518400.000
01058600.000
0482400.000
0208800.000
XX17779400.00001285
XY27425010.00002694
Total315081610.00001989

* Allele frequencies for some sub-continental populations were not computed for genome samples.

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

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 carriers02004006008001.00K1.20K1.40K1.60K1.80K2.00K2.20K2.40KAll 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

Note: This plot may include low-quality genotypes that were excluded from allele counts in the tables above.

Site Quality Metrics

  • Exome
  • Genome
1e11e1.51e21e2.51e31e3.51e41e4.51e51e5.51e61e6.51e71e7.51e81e8.51e91e9.51e10SiteQuality01Genome variants2.009e+3

Value: 2.009e+3 (genome samples)

This is the site quality distribution for all genome variants with 0 <= AF < 0.00005.

Note: These are site-level quality metrics, they may be unpredictable for multi-allelic sites.

Read Data


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