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Genomes
Filters Pass
Allele Count5
Allele Number152184
Allele Frequency0.00003285
Grpmax Filtering AF
(95% confidence)
0.00001972
European (non-Finnish)
Number of homozygotes0
Mean depth of coverage30.9

External Resources

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Genetic Ancestry Group Frequencies

46804400.00005879
14144400.00002413
01061400.000
01527000.000
091200.000
0519200.000
031600.000
0482800.000
0347200.000
0209200.000
XX37783200.00003854
XY27435200.00002690
Total515218400.00003285
Include:

Related Variants

Variant Effect Predictor

This variant falls on 5 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. NLRC4

      1. ENST00000402280.6
        MANE Select transcript for NLRC4
        HGVSp
        p.Lys975Asn
        Domains
        • 3 (Gene3D)
        Polyphen
        benign
        SIFT
        deleterious
      2. ENST00000342905.10
        HGVSp
        p.Lys310Asn
        Domains
        • 3 (Gene3D)
        Polyphen
        benign
        SIFT
        deleterious
      3. ENST00000360906.9
        HGVSp
        p.Lys975Asn
        Domains
        • 3 (Gene3D)
        Polyphen
        benign
        SIFT
        deleterious
  2. 3' UTR

    1. NLRC4

      1. ENST00000404025.3
        HGVSc
        c.*631A>C
      2. ENST00000652197.1
        HGVSc
        c.*655A>C

In Silico Predictors

Transcript-specific predictors SIFT and Polyphen are listed with Variant Effect Predictor annotations.

  • REVEL: 0.0600
  • CADD: 16.7
  • SpliceAI: 0.00 (no_consequence)
  • PrimateAI: 0.276

Genomic Constraint of Surrounding 1kb Region

Genomic constraint values displayed are for the region: 2-32224000-32225000

Read more about this constraint.

ExpectedObservedConstraint
177.1164Z = 0.98
o/e = 0.93
Z Score not constrainedconstrained2.184.0

View the genomic constraint values for the 40kb region surrounding this variant: 2-32204623-32244623

ClinVar

ClinVar Variation ID
656380
Germline classification
Uncertain significance
Review status
criteria provided, multiple submitters, no conflicts (2 stars)
Last evaluated
May 11, 2023

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 quality012345Variant carriers05.00K10.0K15.0K20.0K25.0K30.0K35.0KAll individuals

Site Quality Metrics

  • Exome
  • Genome
1e11e1.51e21e2.51e31e3.51e41e4.51e51e5.51e61e6.51e71e7.51e81e8.51e91e9.51e10SiteQuality05.00M10.0M15.0M20.0M25.0M30.0MGenome variants5.012e+3

Value: 5.012e+3 (genome samples)

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

Read Data


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