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ExomesGenomesTotal
Filters No dataPassNot in exomes
Allele Count-2727
Allele Number-152324152324
Allele Frequency-0.00017730.0001773
Grpmax Filtering AF
(95% confidence)
-0.003507
East Asian
0.003507
East Asian
Number of homozygotes-00

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Genetic Ancestry Group Frequencies

26519400.005006
1482400.0002073
04157600.000
01530400.000
0346800.000
01061200.000
029400.000
06802800.000
091200.000
0211200.000
XX97784800.0001156
XY187447600.0002417
Total2715232400.0001773
Include:

Related Variants

Liftover

The following GRCh37 variant lifts over to this variant:

Variant Effect Predictor

This variant falls on 7 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. intron

    1. SCP2

      1. ENST00000371514.8
        MANE Select transcript for SCP2
        HGVSc
        c.70-5246T>A
      2. ENST00000371509.8
        HGVSc
        c.70-5246T>A
      3. ENST00000371513.9
        HGVSc
        c.70-5246T>A

In Silico Predictors

  • CADD: 3.09
  • SpliceAI: 0.00
  • Pangolin: 0.00
  • phyloP: 0.267
Note For more detailed and up to date SpliceAI and Pangolin predictions, please visit our SpliceAI Lookup browser

Genomic Constraint of Surrounding 1kb Region

Genomic constraint values displayed are for the region: 1-52936000-52937000

Read more about this constraint.

ExpectedObservedConstraint
172.4160Z = 0.95
o/e = 0.93
Z Score not constrainedconstrained2.184.0

View the genomic constraint values for the 40kb region surrounding this variant: 1-52916550-52956550

Age Distribution

  • Exome
  • Genome
  • Variant carriers
  • All individuals
< 3030-3535-4040-4545-5050-5555-6060-6565-7070-7575-80> 80Age0123Variant carriers05001.00K1.50K2.00K2.50K3.00K3.50K4.00KAll individuals

Genotype Quality Metrics

  • Exome
  • Genome
  • Variant carriers
  • All individuals
0-510-1520-2530-3540-4550-5560-6570-7580-8590-95> 100Genotype quality02468101214161820222426Variant carriers02.00K4.00K6.00K8.00K10.0K12.0K14.0K16.0K18.0K20.0KAll individuals

Site Quality Metrics

  • Exome
  • Genome
1e11e1.51e21e2.51e31e3.51e41e4.51e51e5.51e61e6.51e71e7.51e81e8.51e91e9.51e10SiteQuality01.00M2.00M3.00M4.00M5.00M6.00M7.00M8.00M9.00MGenome variants2.965e+4

Value: 2.965e+4 (genome samples)

Site quality approximation for all variants with 0.0001 <= AF < 0.0002.

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

Read Data


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