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GeneBe API Showcase

This page demonstrates how to use the GeneBe API to query variant information. The API provides programmatic access to genomic annotations and variant data.

API presented here should be used for checking single variants. If you want to check many variants at once, please use other API endpoints that you will find in the documentation.

Documentation & Advanced Usage

Complete API documentation:docs.genebe.net/docs/api/overview/

Interactive endpoint tester:api.genebe.net/cloud/gb-api-doc/swagger-ui/

Python client for pandas:pypi.org/project/genebe/

Java CLI for VCF files:github.com/pstawinski/genebe-cli

All tools documented at:docs.genebe.net

API Request Examples for Variant: 6-107154694-G-A (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=107154694&ref=G&alt=A&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "6",
      "pos": 107154694,
      "ref": "G",
      "alt": "A",
      "effect": "synonymous_variant",
      "transcript": "NM_020381.4",
      "consequences": [
        {
          "aa_ref": "A",
          "aa_alt": "A",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 8,
          "exon_rank_end": null,
          "exon_count": 8,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PDSS2",
          "gene_hgnc_id": 23041,
          "hgvs_c": "c.1125C>T",
          "hgvs_p": "p.Ala375Ala",
          "transcript": "NM_020381.4",
          "protein_id": "NP_065114.3",
          "transcript_support_level": null,
          "aa_start": 375,
          "aa_end": null,
          "aa_length": 399,
          "cds_start": 1125,
          "cds_end": null,
          "cds_length": 1200,
          "cdna_start": 1404,
          "cdna_end": null,
          "cdna_length": 3536,
          "mane_select": "ENST00000369037.9",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "A",
          "aa_alt": "A",
          "canonical": true,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 8,
          "exon_rank_end": null,
          "exon_count": 8,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PDSS2",
          "gene_hgnc_id": 23041,
          "hgvs_c": "c.1125C>T",
          "hgvs_p": "p.Ala375Ala",
          "transcript": "ENST00000369037.9",
          "protein_id": "ENSP00000358033.4",
          "transcript_support_level": 1,
          "aa_start": 375,
          "aa_end": null,
          "aa_length": 399,
          "cds_start": 1125,
          "cds_end": null,
          "cds_length": 1200,
          "cdna_start": 1404,
          "cdna_end": null,
          "cdna_length": 3536,
          "mane_select": "NM_020381.4",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "A",
          "aa_alt": "A",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 9,
          "exon_rank_end": null,
          "exon_count": 9,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PDSS2",
          "gene_hgnc_id": 23041,
          "hgvs_c": "c.1323C>T",
          "hgvs_p": "p.Ala441Ala",
          "transcript": "XM_011535956.4",
          "protein_id": "XP_011534258.1",
          "transcript_support_level": null,
          "aa_start": 441,
          "aa_end": null,
          "aa_length": 465,
          "cds_start": 1323,
          "cds_end": null,
          "cds_length": 1398,
          "cdna_start": 1602,
          "cdna_end": null,
          "cdna_length": 3734,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "A",
          "aa_alt": "A",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 8,
          "exon_rank_end": null,
          "exon_count": 8,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PDSS2",
          "gene_hgnc_id": 23041,
          "hgvs_c": "c.1191C>T",
          "hgvs_p": "p.Ala397Ala",
          "transcript": "XM_011535957.4",
          "protein_id": "XP_011534259.1",
          "transcript_support_level": null,
          "aa_start": 397,
          "aa_end": null,
          "aa_length": 421,
          "cds_start": 1191,
          "cds_end": null,
          "cds_length": 1266,
          "cdna_start": 1470,
          "cdna_end": null,
          "cdna_length": 3602,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "A",
          "aa_alt": "A",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 8,
          "exon_rank_end": null,
          "exon_count": 8,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PDSS2",
          "gene_hgnc_id": 23041,
          "hgvs_c": "c.1188C>T",
          "hgvs_p": "p.Ala396Ala",
          "transcript": "XM_011535958.4",
          "protein_id": "XP_011534260.1",
          "transcript_support_level": null,
          "aa_start": 396,
          "aa_end": null,
          "aa_length": 420,
          "cds_start": 1188,
          "cds_end": null,
          "cds_length": 1263,
          "cdna_start": 1467,
          "cdna_end": null,
          "cdna_length": 3599,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "A",
          "aa_alt": "A",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 7,
          "exon_rank_end": null,
          "exon_count": 7,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PDSS2",
          "gene_hgnc_id": 23041,
          "hgvs_c": "c.1017C>T",
          "hgvs_p": "p.Ala339Ala",
          "transcript": "XM_047419096.1",
          "protein_id": "XP_047275052.1",
          "transcript_support_level": null,
          "aa_start": 339,
          "aa_end": null,
          "aa_length": 363,
          "cds_start": 1017,
          "cds_end": null,
          "cds_length": 1092,
          "cdna_start": 1296,
          "cdna_end": null,
          "cdna_length": 3428,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "A",
          "aa_alt": "A",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 7,
          "exon_rank_end": null,
          "exon_count": 7,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PDSS2",
          "gene_hgnc_id": 23041,
          "hgvs_c": "c.993C>T",
          "hgvs_p": "p.Ala331Ala",
          "transcript": "XM_011535959.4",
          "protein_id": "XP_011534261.1",
          "transcript_support_level": null,
          "aa_start": 331,
          "aa_end": null,
          "aa_length": 355,
          "cds_start": 993,
          "cds_end": null,
          "cds_length": 1068,
          "cdna_start": 1272,
          "cdna_end": null,
          "cdna_length": 3404,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "A",
          "aa_alt": "A",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 7,
          "exon_rank_end": null,
          "exon_count": 7,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PDSS2",
          "gene_hgnc_id": 23041,
          "hgvs_c": "c.990C>T",
          "hgvs_p": "p.Ala330Ala",
          "transcript": "XM_047419097.1",
          "protein_id": "XP_047275053.1",
          "transcript_support_level": null,
          "aa_start": 330,
          "aa_end": null,
          "aa_length": 354,
          "cds_start": 990,
          "cds_end": null,
          "cds_length": 1065,
          "cdna_start": 1269,
          "cdna_end": null,
          "cdna_length": 3401,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "A",
          "aa_alt": "A",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 9,
          "exon_rank_end": null,
          "exon_count": 9,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PDSS2",
          "gene_hgnc_id": 23041,
          "hgvs_c": "c.915C>T",
          "hgvs_p": "p.Ala305Ala",
          "transcript": "XM_011535960.4",
          "protein_id": "XP_011534262.1",
          "transcript_support_level": null,
          "aa_start": 305,
          "aa_end": null,
          "aa_length": 329,
          "cds_start": 915,
          "cds_end": null,
          "cds_length": 990,
          "cdna_start": 1224,
          "cdna_end": null,
          "cdna_length": 3356,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "A",
          "aa_alt": "A",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 9,
          "exon_rank_end": null,
          "exon_count": 9,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PDSS2",
          "gene_hgnc_id": 23041,
          "hgvs_c": "c.867C>T",
          "hgvs_p": "p.Ala289Ala",
          "transcript": "XM_047419098.1",
          "protein_id": "XP_047275054.1",
          "transcript_support_level": null,
          "aa_start": 289,
          "aa_end": null,
          "aa_length": 313,
          "cds_start": 867,
          "cds_end": null,
          "cds_length": 942,
          "cdna_start": 1073,
          "cdna_end": null,
          "cdna_length": 3205,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "A",
          "aa_alt": "A",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 6,
          "exon_rank_end": null,
          "exon_count": 6,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PDSS2",
          "gene_hgnc_id": 23041,
          "hgvs_c": "c.858C>T",
          "hgvs_p": "p.Ala286Ala",
          "transcript": "XM_047419099.1",
          "protein_id": "XP_047275055.1",
          "transcript_support_level": null,
          "aa_start": 286,
          "aa_end": null,
          "aa_length": 310,
          "cds_start": 858,
          "cds_end": null,
          "cds_length": 933,
          "cdna_start": 1137,
          "cdna_end": null,
          "cdna_length": 3269,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "A",
          "aa_alt": "A",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 6,
          "exon_rank_end": null,
          "exon_count": 6,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PDSS2",
          "gene_hgnc_id": 23041,
          "hgvs_c": "c.819C>T",
          "hgvs_p": "p.Ala273Ala",
          "transcript": "XM_011535961.4",
          "protein_id": "XP_011534263.1",
          "transcript_support_level": null,
          "aa_start": 273,
          "aa_end": null,
          "aa_length": 297,
          "cds_start": 819,
          "cds_end": null,
          "cds_length": 894,
          "cdna_start": 1098,
          "cdna_end": null,
          "cdna_length": 3230,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "A",
          "aa_alt": "A",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 9,
          "exon_rank_end": null,
          "exon_count": 9,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PDSS2",
          "gene_hgnc_id": 23041,
          "hgvs_c": "c.783C>T",
          "hgvs_p": "p.Ala261Ala",
          "transcript": "XM_047419100.1",
          "protein_id": "XP_047275056.1",
          "transcript_support_level": null,
          "aa_start": 261,
          "aa_end": null,
          "aa_length": 285,
          "cds_start": 783,
          "cds_end": null,
          "cds_length": 858,
          "cdna_start": 1286,
          "cdna_end": null,
          "cdna_length": 3418,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "A",
          "aa_alt": "A",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 5,
          "exon_rank_end": null,
          "exon_count": 5,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PDSS2",
          "gene_hgnc_id": 23041,
          "hgvs_c": "c.684C>T",
          "hgvs_p": "p.Ala228Ala",
          "transcript": "XM_047419101.1",
          "protein_id": "XP_047275057.1",
          "transcript_support_level": null,
          "aa_start": 228,
          "aa_end": null,
          "aa_length": 252,
          "cds_start": 684,
          "cds_end": null,
          "cds_length": 759,
          "cdna_start": 963,
          "cdna_end": null,
          "cdna_length": 3095,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        }
      ],
      "gene_symbol": "PDSS2",
      "gene_hgnc_id": 23041,
      "dbsnp": "rs1554245194",
      "frequency_reference_population": 6.8409935e-7,
      "hom_count_reference_population": 0,
      "allele_count_reference_population": 1,
      "gnomad_exomes_af": 6.84099e-7,
      "gnomad_genomes_af": null,
      "gnomad_exomes_ac": 1,
      "gnomad_genomes_ac": null,
      "gnomad_exomes_homalt": 0,
      "gnomad_genomes_homalt": null,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": -0.3100000023841858,
      "computational_prediction_selected": "Benign",
      "computational_source_selected": "BayesDel_noAF",
      "splice_score_selected": 0,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": null,
      "revel_prediction": null,
      "alphamissense_score": null,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": -0.31,
      "bayesdelnoaf_prediction": "Benign",
      "phylop100way_score": 4.357,
      "phylop100way_prediction": "Uncertain_significance",
      "spliceai_max_score": 0,
      "spliceai_max_prediction": "Benign",
      "dbscsnv_ada_score": null,
      "dbscsnv_ada_prediction": null,
      "apogee2_score": null,
      "apogee2_prediction": null,
      "mitotip_score": null,
      "mitotip_prediction": null,
      "acmg_score": 0,
      "acmg_classification": "Uncertain_significance",
      "acmg_criteria": "PM2,BP4_Moderate",
      "acmg_by_gene": [
        {
          "score": 0,
          "benign_score": 2,
          "pathogenic_score": 2,
          "criteria": [
            "PM2",
            "BP4_Moderate"
          ],
          "verdict": "Uncertain_significance",
          "transcript": "NM_020381.4",
          "gene_symbol": "PDSS2",
          "hgnc_id": 23041,
          "effects": [
            "synonymous_variant"
          ],
          "inheritance_mode": "AR",
          "hgvs_c": "c.1125C>T",
          "hgvs_p": "p.Ala375Ala"
        }
      ],
      "clinvar_disease": "",
      "clinvar_classification": "",
      "clinvar_review_status": "",
      "clinvar_submissions_summary": "",
      "phenotype_combined": null,
      "pathogenicity_classification_combined": null,
      "custom_annotations": null
    }
  ],
  "message": null
}