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ExomesGenomesTotal
Filters PassPass
Allele Count5794881067
Allele Number14617001522241613924
Allele Frequency0.00039610.0032060.0006611
Grpmax Filtering AF
(95% confidence)
0.01210
African/African American
0.01026
African/African American
0.01135
African/African American
Number of homozygotes10414

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Genetic Ancestry Group Frequencies

90075016120.01200
21606200.003464
726248220.001152
456001000.0007499
59107800.00005490
24117989000.00002034
02960800.000
04486200.000
06400400.000
091200.000
XX58781237680.0007226
XY48080154860.0005988
Total10671613924140.0006611
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 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. synonymous

    1. SNTG2

      1. ENST00000308624.10
        MANE Select transcript for SNTG2
        HGVSp
        p.Ser221Ser
        Domains
        • PTHR10554 (PANTHER)
        • SSF50729 (Superfamily)
      2. ENST00000407292.1
        HGVSp
        p.Ser94Ser
        Domains
        • PTHR10554 (PANTHER)
  2. non coding transcript exon

    1. SNTG2

      1. ENST00000463442.5
        HGVSc
        n.541C>G
      2. ENST00000467759.5
        HGVSc
        n.295C>G
      3. ENST00000494178.1
        HGVSc
        n.415C>G
  3. intron

    1. SNTG2

      1. ENST00000475201.5
        HGVSc
        n.224-10708C>G

In Silico Predictors

  • CADD: 1.96
  • SpliceAI: 0.0100
  • Pangolin: 0.0300
  • phyloP: -8.76
Note For more detailed and up to date SpliceAI and Pangolin predictions, please visit our SpliceAI Lookup browser

Genomic Constraint of Surrounding 1kb Region

Genomic constraint values displayed are for the region: 2-1209000-1210000

Read more about this constraint.

ExpectedObservedConstraint
100.188Z = 1.2
o/e = 0.88
Z Score not constrainedconstrained2.184.0

View the genomic constraint values for the 40kb region surrounding this variant: 2-1189174-1229174

ClinVar

ClinVar Variation ID
724334
Conditions
not provided
Germline classification
Benign
Review status
criteria provided, multiple submitters, no conflicts (2 stars)
Last evaluated
June 6, 2018

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> 80Age0102030405060708090100Variant 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 quality01002003004005006007008009001.00KVariant carriers050.0K100K150K200K250K300K350K400KAll 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 variants0500K1.00M1.50M2.00M2.50M3.00MGenome variants3.782e+59.380e+5

Value: 9.380e+5 (exome samples), 3.782e+5 (genome samples)

Site quality approximation for all variants with 0.002 <= AF < 0.005.

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

Read Data


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