Help us continue to improve gnomAD by taking 5 minutes to fill out our user survey.
ExomesGenomesTotal
Filters PassPassDiscrepant frequencies
Allele Count22191382357
Allele Number14618021522541614056
Allele Frequency0.0015180.00090640.001460
Grpmax Filtering AF
(95% confidence)
0.001835
European (non-Finnish)
0.001317
European (non-Finnish)
0.001817
European (non-Finnish)
Number of homozygotes415

External Resources

Feedback

Report an issue with this variant

Genetic Ancestry Group Frequencies

2222118004440.001883
466248800.0007361
386001610.0006332
3606400.0004947
237495200.0003069
179109200.0001866
52960600.0001689
36398400.00004689
04489800.000
091200.000
XX119981248640.001476
XY115880157010.001445
Total2357161405650.001460
Include:

Related Variants

Other Alternate Alleles

This variant is multiallelic. Other alternate alleles are:

Liftover

The following GRCh37 variant lifts over to this variant:

Variant Effect Predictor

This variant falls on 1 transcript in 1 gene.

Note The gene symbols shown below are provided by VEP and may differ from the symbol shown on gene pages.

  1. synonymous

    1. NTNG2

      1. ENST00000393229.4
        MANE Select transcript for NTNG2
        HGVSp
        p.Leu9Leu
        Domains
        • 3zyg (ENSP_mappings)

In Silico Predictors

  • CADD: 10.2
  • SpliceAI: 0.00
  • Pangolin: 0.0100
  • phyloP: 5.76
Note For more detailed and up to date SpliceAI and Pangolin predictions, please visit our SpliceAI Lookup browser

Genomic Constraint of Surrounding 1kb Region

This variant does not have non coding constraint data for the surrounding region.

ClinVar

ClinVar Variation ID
739685
Conditions
not provided
Germline classification
Likely benign
Review status
criteria provided, multiple submitters, no conflicts (2 stars)
Last evaluated
November 1, 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> 80Age050100150200250300350400Variant carriers010.0K20.0K30.0K40.0K50.0K60.0K70.0K80.0K90.0K100K110KAll individuals

Genotype Quality Metrics

  • Exome
  • Genome
  • Variant carriers
  • All individuals
0-510-1520-2530-3540-4550-5560-6570-7580-8590-95> 100Genotype quality02004006008001.00K1.20K1.40K1.60K1.80K2.00K2.20KVariant carriers050.0K100K150K200K250K300K350K400KAll individuals

Site Quality Metrics

  • Exome
  • Genome
1e11e1.51e21e2.51e31e3.51e41e4.51e51e5.51e61e6.51e71e7.51e81e8.51e91e9.51e10SiteQuality05.00K10.0K15.0K20.0K25.0K30.0K35.0K40.0KExome variants0500K1.00M1.50M2.00M2.50M3.00M3.50M4.00MGenome variants1.641e+52.350e+6

Value: 2.350e+6 (exome samples), 1.641e+5 (genome samples)

Site quality approximation for all variants with 0.0005 <= AF < 0.001.

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

Read Data


Always load read data