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ExomesGenomesTotal
Filters PassPass
Allele Count34948397
Allele Number14555901522361607826
Allele Frequency0.00023980.00031530.0002469
Grpmax Filtering AF
(95% confidence)
0.004559
East Asian
0.004014
East Asian
0.004645
East Asian
Number of homozygotes000

External Resources

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Genetic Ancestry Group Frequencies

2324467200.005193
1022950400.003457
259087800.0002751
166225600.0002570
1605200.0001652
15981400.00001672
19117508600.00001617
17491600.00001335
06373600.000
091200.000
XX21281032400.0002616
XY18579750200.0002320
Total397160782600.0002469
Include:

Related Variants

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. intron

    1. LETM1

      1. ENST00000302787.3
        MANE Select transcript for LETM1
        HGVSc
        c.1931+20C>T

In Silico Predictors

  • CADD: 0.410
  • SpliceAI: 0.00
  • Pangolin: 0.00
  • phyloP: -3.49
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
1900773
Conditions
not provided
Germline classification
Benign
Review status
criteria provided, single submitter (1 star)
Last evaluated
September 13, 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> 80Age05101520253035Variant 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 quality050100150200250300350Variant carriers050.0K100K150K200K250K300K350KAll individuals

Site Quality Metrics

  • Exome
  • Genome
1e11e1.51e21e2.51e31e3.51e41e4.51e51e5.51e61e6.51e71e7.51e81e8.51e91e9.51e10SiteQuality010.0K20.0K30.0K40.0K50.0K60.0K70.0K80.0K90.0K100K110K120KExome variants0500K1.00M1.50M2.00M2.50M3.00M3.50M4.00M4.50M5.00M5.50M6.00MGenome variants4.349e+43.305e+5

Value: 3.305e+5 (exome samples), 4.349e+4 (genome samples)

Site quality approximation for all variants with 0.0002 <= AF < 0.0005.

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

Read Data


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