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Genomes
Filters Pass
Allele Count215
Allele Number152058
Allele Frequency0.001414
Grpmax Filtering AF
(95% confidence)
0.001849
European (non-Finnish)
Number of homozygotes2
Mean depth of coverage31.1

External Resources

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Genetic Ancestry Group Frequencies

21346800.006055
331060000.003113
1456801220.002132
2209200.0009560
101526000.0006553
44139800.00009662
091200.000
0518600.000
031600.000
0481400.000
XX1137778420.001453
XY1027427400.001373
Total21515205820.001414
Include:

Related Variants

Variant Effect Predictor

This variant falls on 8 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. SCN11A

      1. ENST00000302328.9
        MANE Select transcript for SCN11A
        HGVSp
        p.Gly1736Val
        Domains
        • 1 (Gene3D)
        • PTHR10037 (PANTHER)
        Polyphen
        benign
        SIFT
        deleterious
      2. ENST00000668754.1
        Ensembl canonical transcript for SCN11A
        HGVSp
        p.Gly1736Val
        Domains
        • 1 (Gene3D)
        • PTHR10037 (PANTHER)
        Polyphen
        benign
        SIFT
        deleterious
      3. ENST00000456224.7
        HGVSp
        p.Gly1698Val
        Domains
        • 1 (Gene3D)
        • PTHR10037 (PANTHER)
        Polyphen
        benign
        SIFT
        deleterious
  2. 3' UTR

    1. SCN11A

      1. ENST00000675223.1
        HGVSc
        c.*951G>T
      2. ENST00000675672.1
        HGVSc
        c.*2378G>T
      3. ENST00000676045.1
        HGVSc
        c.*4924G>T

In Silico Predictors

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

  • REVEL: 0.264
  • CADD: 19.6
  • SpliceAI: 0.00 (no_consequence)
  • PrimateAI: 0.308

Genomic Constraint of Surrounding 1kb Region

Genomic constraint values displayed are for the region: 3-38846000-38847000

Read more about this constraint.

ExpectedObservedConstraint
98.997Z = 0.19
o/e = 0.98
Z Score not constrainedconstrained2.184.0

View the genomic constraint values for the 40kb region surrounding this variant: 3-38826863-38866863

ClinVar

ClinVar Variation ID
474745
Germline classification
Benign/Likely benign
Review status
criteria provided, multiple submitters, no conflicts (2 stars)
Last evaluated
January 19, 2024

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> 80Age01234567891011121314Variant 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 quality020406080100120140160180200Variant carriers02.00K4.00K6.00K8.00K10.0K12.0K14.0K16.0K18.0KAll individuals

Site Quality Metrics

  • Exome
  • Genome
1e11e1.51e21e2.51e31e3.51e41e4.51e51e5.51e61e6.51e71e7.51e81e8.51e91e9.51e10SiteQuality0200K400K600K800K1.00M1.20M1.40M1.60M1.80M2.00M2.20M2.40M2.60M2.80MGenome variants1.674e+5

Value: 1.674e+5 (genome samples)

Site quality approximation for all variants with 0.001 <= AF < 0.002.

Read Data


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