Help us continue to improve gnomAD by taking 5 minutes to fill out our user survey.
ExomesGenomesTotal
Filters PassPass
Allele Count10609535715966
Allele Number14585121522461610758
Allele Frequency0.0072740.035190.009912
Grpmax Filtering AF
(95% confidence)
0.1141
African/African American
0.1096
African/African American
0.1125
African/African American
Number of homozygotes299253552

External Resources

Feedback

Report an issue with this variant

Genetic Ancestry Group Frequencies

Note Local ancestry data is available for this variant by selecting the tab below. See our blog post on local ancestry inference for Admixed American samples in gnomAD for more information.

8568748425000.1145
121604820.02001
83662388170.01340
73160002100.01218
2032956610.006866
52131177166140.004428
2759099480.003022
196401800.0002968
04482400.000
091000.000
XX85328104603080.01053
XY74348002982440.009289
Total1596616107585520.009912
Include:

Related Variants

Liftover

The following GRCh37 variant lifts over to this variant:

Variant Effect Predictor

This variant falls on 6 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. synonymous

    1. SEC24D

      1. ENST00000280551.11
        MANE Select transcript for SEC24D
        HGVSp
        p.Leu798Leu
        Domains
      2. ENST00000419654.6
        HGVSp
        p.Leu354Leu
        Domains
        • 1 (Gene3D)
      3. ENST00000511481.5
        HGVSp
        p.Leu429Leu
        Domains
  2. non coding transcript exon

    1. SEC24D

      1. ENST00000502526.1
        HGVSc
        n.92C>T
      2. ENST00000505134.5
        HGVSc
        n.1682C>T
  3. 3' UTR

    1. SEC24D

      1. ENST00000514561.5
        HGVSc
        c.*2801C>T

In Silico Predictors

  • CADD: 0.115
  • SpliceAI: 0.00
  • Pangolin: 0.00
  • phyloP: -1.70
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: 4-118738000-118739000

Read more about this constraint.

ExpectedObservedConstraint
177.4165Z = 0.93
o/e = 0.93
Z Score not constrainedconstrained2.184.0

View the genomic constraint values for the 40kb region surrounding this variant: 4-118718363-118758363

ClinVar

ClinVar Variation ID
1242560
Conditions
not provided
Germline classification
Benign
Review status
criteria provided, multiple submitters, no conflicts (2 stars)
Last evaluated
January 25, 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> 80Age02004006008001.00K1.20K1.40KVariant 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 quality02.00K4.00K6.00K8.00K10.0K12.0K14.0KVariant carriers050.0K100K150K200K250K300K350KAll individuals

Site Quality Metrics

  • Exome
  • Genome
1e11e1.51e21e2.51e31e3.51e41e4.51e51e5.51e61e6.51e71e7.51e81e8.51e91e9.51e10SiteQuality02.00K4.00K6.00K8.00K10.0K12.0K14.0K16.0K18.0K20.0K22.0K24.0K26.0K28.0KExome variants0200K400K600K800K1.00M1.20M1.40MGenome variants4.923e+68.053e+6

Value: 8.053e+6 (exome samples), 4.923e+6 (genome samples)

Site quality approximation for all variants with 0.02 <= AF < 0.05.

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

Read Data


Always load read data