← Back to variant description

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: 5-179799971-G-C (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=179799971&ref=G&alt=C&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "5",
      "pos": 179799971,
      "ref": "G",
      "alt": "C",
      "effect": "missense_variant",
      "transcript": "NM_014275.5",
      "consequences": [
        {
          "aa_ref": "S",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 8,
          "exon_rank_end": null,
          "exon_count": 15,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MGAT4B",
          "gene_hgnc_id": 7048,
          "hgvs_c": "c.893C>G",
          "hgvs_p": "p.Ser298Cys",
          "transcript": "NM_014275.5",
          "protein_id": "NP_055090.1",
          "transcript_support_level": null,
          "aa_start": 298,
          "aa_end": null,
          "aa_length": 548,
          "cds_start": 893,
          "cds_end": null,
          "cds_length": 1647,
          "cdna_start": 1176,
          "cdna_end": null,
          "cdna_length": 2365,
          "mane_select": "ENST00000292591.12",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "S",
          "aa_alt": "C",
          "canonical": true,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 8,
          "exon_rank_end": null,
          "exon_count": 15,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MGAT4B",
          "gene_hgnc_id": 7048,
          "hgvs_c": "c.893C>G",
          "hgvs_p": "p.Ser298Cys",
          "transcript": "ENST00000292591.12",
          "protein_id": "ENSP00000292591.7",
          "transcript_support_level": 1,
          "aa_start": 298,
          "aa_end": null,
          "aa_length": 548,
          "cds_start": 893,
          "cds_end": null,
          "cds_length": 1647,
          "cdna_start": 1176,
          "cdna_end": null,
          "cdna_length": 2365,
          "mane_select": "NM_014275.5",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "S",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 7,
          "exon_rank_end": null,
          "exon_count": 12,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MGAT4B",
          "gene_hgnc_id": 7048,
          "hgvs_c": "c.734C>G",
          "hgvs_p": "p.Ser245Cys",
          "transcript": "ENST00000519836.5",
          "protein_id": "ENSP00000430721.1",
          "transcript_support_level": 1,
          "aa_start": 245,
          "aa_end": null,
          "aa_length": 428,
          "cds_start": 734,
          "cds_end": null,
          "cds_length": 1287,
          "cdna_start": 736,
          "cdna_end": null,
          "cdna_length": 1686,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "S",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 5,
          "exon_rank_end": null,
          "exon_count": 12,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MGAT4B",
          "gene_hgnc_id": 7048,
          "hgvs_c": "c.368C>G",
          "hgvs_p": "p.Ser123Cys",
          "transcript": "ENST00000518778.5",
          "protein_id": "ENSP00000428906.1",
          "transcript_support_level": 1,
          "aa_start": 123,
          "aa_end": null,
          "aa_length": 372,
          "cds_start": 368,
          "cds_end": null,
          "cds_length": 1119,
          "cdna_start": 369,
          "cdna_end": null,
          "cdna_length": 1568,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "S",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 7,
          "exon_rank_end": null,
          "exon_count": 14,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MGAT4B",
          "gene_hgnc_id": 7048,
          "hgvs_c": "c.938C>G",
          "hgvs_p": "p.Ser313Cys",
          "transcript": "NM_054013.3",
          "protein_id": "NP_463459.1",
          "transcript_support_level": null,
          "aa_start": 313,
          "aa_end": null,
          "aa_length": 563,
          "cds_start": 938,
          "cds_end": null,
          "cds_length": 1692,
          "cdna_start": 1702,
          "cdna_end": null,
          "cdna_length": 2904,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "S",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 7,
          "exon_rank_end": null,
          "exon_count": 14,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MGAT4B",
          "gene_hgnc_id": 7048,
          "hgvs_c": "c.938C>G",
          "hgvs_p": "p.Ser313Cys",
          "transcript": "ENST00000337755.9",
          "protein_id": "ENSP00000338487.5",
          "transcript_support_level": 2,
          "aa_start": 313,
          "aa_end": null,
          "aa_length": 563,
          "cds_start": 938,
          "cds_end": null,
          "cds_length": 1692,
          "cdna_start": 1825,
          "cdna_end": null,
          "cdna_length": 3027,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "S",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 8,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MGAT4B",
          "gene_hgnc_id": 7048,
          "hgvs_c": "c.287C>G",
          "hgvs_p": "p.Ser96Cys",
          "transcript": "ENST00000520875.5",
          "protein_id": "ENSP00000430723.1",
          "transcript_support_level": 5,
          "aa_start": 96,
          "aa_end": null,
          "aa_length": 320,
          "cds_start": 287,
          "cds_end": null,
          "cds_length": 963,
          "cdna_start": 288,
          "cdna_end": null,
          "cdna_length": 964,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "S",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 4,
          "exon_rank_end": null,
          "exon_count": 10,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MGAT4B",
          "gene_hgnc_id": 7048,
          "hgvs_c": "c.320C>G",
          "hgvs_p": "p.Ser107Cys",
          "transcript": "ENST00000518980.5",
          "protein_id": "ENSP00000431093.1",
          "transcript_support_level": 5,
          "aa_start": 107,
          "aa_end": null,
          "aa_length": 306,
          "cds_start": 320,
          "cds_end": null,
          "cds_length": 921,
          "cdna_start": 321,
          "cdna_end": null,
          "cdna_length": 983,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "S",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 4,
          "exon_rank_end": null,
          "exon_count": 9,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MGAT4B",
          "gene_hgnc_id": 7048,
          "hgvs_c": "c.326C>G",
          "hgvs_p": "p.Ser109Cys",
          "transcript": "ENST00000518867.5",
          "protein_id": "ENSP00000428764.1",
          "transcript_support_level": 5,
          "aa_start": 109,
          "aa_end": null,
          "aa_length": 242,
          "cds_start": 326,
          "cds_end": null,
          "cds_length": 731,
          "cdna_start": 327,
          "cdna_end": null,
          "cdna_length": 732,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "S",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 8,
          "exon_rank_end": null,
          "exon_count": 9,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MGAT4B",
          "gene_hgnc_id": 7048,
          "hgvs_c": "c.458C>G",
          "hgvs_p": "p.Ser153Cys",
          "transcript": "ENST00000523108.5",
          "protein_id": "ENSP00000427995.1",
          "transcript_support_level": 5,
          "aa_start": 153,
          "aa_end": null,
          "aa_length": 199,
          "cds_start": 458,
          "cds_end": null,
          "cds_length": 600,
          "cdna_start": 938,
          "cdna_end": null,
          "cdna_length": 1080,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "S",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 8,
          "exon_rank_end": null,
          "exon_count": 15,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MGAT4B",
          "gene_hgnc_id": 7048,
          "hgvs_c": "c.458C>G",
          "hgvs_p": "p.Ser153Cys",
          "transcript": "XM_024454349.2",
          "protein_id": "XP_024310117.1",
          "transcript_support_level": null,
          "aa_start": 153,
          "aa_end": null,
          "aa_length": 403,
          "cds_start": 458,
          "cds_end": null,
          "cds_length": 1212,
          "cdna_start": 4327,
          "cdna_end": null,
          "cdna_length": 5516,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": false,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 4,
          "exon_rank_end": null,
          "exon_count": 6,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MGAT4B",
          "gene_hgnc_id": 7048,
          "hgvs_c": "n.379C>G",
          "hgvs_p": null,
          "transcript": "ENST00000518702.5",
          "protein_id": null,
          "transcript_support_level": 3,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 542,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": false,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 3,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MGAT4B",
          "gene_hgnc_id": 7048,
          "hgvs_c": "n.280C>G",
          "hgvs_p": null,
          "transcript": "ENST00000520822.5",
          "protein_id": null,
          "transcript_support_level": 2,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 745,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": false,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 2,
          "exon_rank_end": null,
          "exon_count": 2,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MGAT4B",
          "gene_hgnc_id": 7048,
          "hgvs_c": "n.346C>G",
          "hgvs_p": null,
          "transcript": "ENST00000521855.1",
          "protein_id": null,
          "transcript_support_level": 2,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 593,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": false,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 5,
          "exon_rank_end": null,
          "exon_count": 10,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MGAT4B",
          "gene_hgnc_id": 7048,
          "hgvs_c": "n.391C>G",
          "hgvs_p": null,
          "transcript": "ENST00000523382.5",
          "protein_id": null,
          "transcript_support_level": 3,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 778,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "downstream_gene_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 6,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MGAT4B",
          "gene_hgnc_id": 7048,
          "hgvs_c": "n.*330C>G",
          "hgvs_p": null,
          "transcript": "ENST00000520918.5",
          "protein_id": "ENSP00000430376.1",
          "transcript_support_level": 3,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 799,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        }
      ],
      "gene_symbol": "MGAT4B",
      "gene_hgnc_id": 7048,
      "dbsnp": "rs747182303",
      "frequency_reference_population": 0.000012315945,
      "hom_count_reference_population": 0,
      "allele_count_reference_population": 18,
      "gnomad_exomes_af": 0.0000123159,
      "gnomad_genomes_af": null,
      "gnomad_exomes_ac": 18,
      "gnomad_genomes_ac": null,
      "gnomad_exomes_homalt": 0,
      "gnomad_genomes_homalt": null,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": 0.9083734750747681,
      "computational_prediction_selected": "Pathogenic",
      "computational_source_selected": "MetaRNN",
      "splice_score_selected": 0.019999999552965164,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": 0.411,
      "revel_prediction": "Uncertain_significance",
      "alphamissense_score": 0.7991,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": 0.15,
      "bayesdelnoaf_prediction": "Pathogenic",
      "phylop100way_score": 9.906,
      "phylop100way_prediction": "Pathogenic",
      "spliceai_max_score": 0.02,
      "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": 2,
      "acmg_classification": "Uncertain_significance",
      "acmg_criteria": "PP3_Moderate",
      "acmg_by_gene": [
        {
          "score": 2,
          "benign_score": 0,
          "pathogenic_score": 2,
          "criteria": [
            "PP3_Moderate"
          ],
          "verdict": "Uncertain_significance",
          "transcript": "NM_014275.5",
          "gene_symbol": "MGAT4B",
          "hgnc_id": 7048,
          "effects": [
            "missense_variant"
          ],
          "inheritance_mode": "AR",
          "hgvs_c": "c.893C>G",
          "hgvs_p": "p.Ser298Cys"
        }
      ],
      "clinvar_disease": "not specified",
      "clinvar_classification": "Uncertain significance",
      "clinvar_review_status": "criteria provided, single submitter",
      "clinvar_submissions_summary": "US:1",
      "phenotype_combined": "not specified",
      "pathogenicity_classification_combined": "Uncertain significance",
      "custom_annotations": null
    }
  ],
  "message": null
}