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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: 11-64210718-C-T (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=11&pos=64210718&ref=C&alt=T&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "11",
      "pos": 64210718,
      "ref": "C",
      "alt": "T",
      "effect": "5_prime_UTR_premature_start_codon_gain_variant",
      "transcript": "NM_001382364.1",
      "consequences": [
        {
          "aa_ref": "R",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 15,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "FERMT3",
          "gene_hgnc_id": 23151,
          "hgvs_c": "c.268C>T",
          "hgvs_p": "p.Arg90Cys",
          "transcript": "NM_031471.6",
          "protein_id": "NP_113659.3",
          "transcript_support_level": null,
          "aa_start": 90,
          "aa_end": null,
          "aa_length": 663,
          "cds_start": 268,
          "cds_end": null,
          "cds_length": 1992,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": "ENST00000345728.10",
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_031471.6"
        },
        {
          "aa_ref": "R",
          "aa_alt": "C",
          "canonical": true,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 15,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "FERMT3",
          "gene_hgnc_id": 23151,
          "hgvs_c": "c.268C>T",
          "hgvs_p": "p.Arg90Cys",
          "transcript": "ENST00000345728.10",
          "protein_id": "ENSP00000339950.5",
          "transcript_support_level": 1,
          "aa_start": 90,
          "aa_end": null,
          "aa_length": 663,
          "cds_start": 268,
          "cds_end": null,
          "cds_length": 1992,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": "NM_031471.6",
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000345728.10"
        },
        {
          "aa_ref": "R",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 15,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "FERMT3",
          "gene_hgnc_id": 23151,
          "hgvs_c": "c.268C>T",
          "hgvs_p": "p.Arg90Cys",
          "transcript": "ENST00000279227.10",
          "protein_id": "ENSP00000279227.5",
          "transcript_support_level": 1,
          "aa_start": 90,
          "aa_end": null,
          "aa_length": 667,
          "cds_start": 268,
          "cds_end": null,
          "cds_length": 2004,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000279227.10"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "5_prime_UTR_premature_start_codon_gain_variant"
          ],
          "exon_rank": 2,
          "exon_rank_end": null,
          "exon_count": 14,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "FERMT3",
          "gene_hgnc_id": 23151,
          "hgvs_c": "c.-273C>T",
          "hgvs_p": null,
          "transcript": "NM_001382364.1",
          "protein_id": "NP_001369293.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 487,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 1464,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_001382364.1"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "5_prime_UTR_premature_start_codon_gain_variant"
          ],
          "exon_rank": 2,
          "exon_rank_end": null,
          "exon_count": 14,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "FERMT3",
          "gene_hgnc_id": 23151,
          "hgvs_c": "c.-273C>T",
          "hgvs_p": null,
          "transcript": "NM_001382363.1",
          "protein_id": "NP_001369292.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 483,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 1452,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_001382363.1"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "5_prime_UTR_premature_start_codon_gain_variant"
          ],
          "exon_rank": 2,
          "exon_rank_end": null,
          "exon_count": 14,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "FERMT3",
          "gene_hgnc_id": 23151,
          "hgvs_c": "c.-273C>T",
          "hgvs_p": null,
          "transcript": "ENST00000541252.2",
          "protein_id": "ENSP00000438885.2",
          "transcript_support_level": 3,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 483,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 1452,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000541252.2"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "5_prime_UTR_premature_start_codon_gain_variant"
          ],
          "exon_rank": 2,
          "exon_rank_end": null,
          "exon_count": 14,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "FERMT3",
          "gene_hgnc_id": 23151,
          "hgvs_c": "c.-273C>T",
          "hgvs_p": null,
          "transcript": "ENST00000698874.1",
          "protein_id": "ENSP00000513999.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 483,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 1452,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000698874.1"
        },
        {
          "aa_ref": "R",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 15,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "FERMT3",
          "gene_hgnc_id": 23151,
          "hgvs_c": "c.268C>T",
          "hgvs_p": "p.Arg90Cys",
          "transcript": "ENST00000698865.1",
          "protein_id": "ENSP00000513992.1",
          "transcript_support_level": null,
          "aa_start": 90,
          "aa_end": null,
          "aa_length": 670,
          "cds_start": 268,
          "cds_end": null,
          "cds_length": 2013,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000698865.1"
        },
        {
          "aa_ref": "R",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 15,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "FERMT3",
          "gene_hgnc_id": 23151,
          "hgvs_c": "c.268C>T",
          "hgvs_p": "p.Arg90Cys",
          "transcript": "ENST00000962569.1",
          "protein_id": "ENSP00000632628.1",
          "transcript_support_level": null,
          "aa_start": 90,
          "aa_end": null,
          "aa_length": 670,
          "cds_start": 268,
          "cds_end": null,
          "cds_length": 2013,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000962569.1"
        },
        {
          "aa_ref": "R",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 15,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "FERMT3",
          "gene_hgnc_id": 23151,
          "hgvs_c": "c.268C>T",
          "hgvs_p": "p.Arg90Cys",
          "transcript": "NM_001382362.1",
          "protein_id": "NP_001369291.1",
          "transcript_support_level": null,
          "aa_start": 90,
          "aa_end": null,
          "aa_length": 667,
          "cds_start": 268,
          "cds_end": null,
          "cds_length": 2004,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_001382362.1"
        },
        {
          "aa_ref": "R",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 15,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "FERMT3",
          "gene_hgnc_id": 23151,
          "hgvs_c": "c.268C>T",
          "hgvs_p": "p.Arg90Cys",
          "transcript": "NM_178443.3",
          "protein_id": "NP_848537.1",
          "transcript_support_level": null,
          "aa_start": 90,
          "aa_end": null,
          "aa_length": 667,
          "cds_start": 268,
          "cds_end": null,
          "cds_length": 2004,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_178443.3"
        },
        {
          "aa_ref": "R",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 15,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "FERMT3",
          "gene_hgnc_id": 23151,
          "hgvs_c": "c.268C>T",
          "hgvs_p": "p.Arg90Cys",
          "transcript": "ENST00000698860.1",
          "protein_id": "ENSP00000513988.1",
          "transcript_support_level": null,
          "aa_start": 90,
          "aa_end": null,
          "aa_length": 667,
          "cds_start": 268,
          "cds_end": null,
          "cds_length": 2004,
          "cdna_start": null,
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          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000698860.1"
        },
        {
          "aa_ref": "R",
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          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 15,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "FERMT3",
          "gene_hgnc_id": 23151,
          "hgvs_c": "c.268C>T",
          "hgvs_p": "p.Arg90Cys",
          "transcript": "NM_001382361.1",
          "protein_id": "NP_001369290.1",
          "transcript_support_level": null,
          "aa_start": 90,
          "aa_end": null,
          "aa_length": 663,
          "cds_start": 268,
          "cds_end": null,
          "cds_length": 1992,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
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          "biotype": "protein_coding",
          "feature": "NM_001382361.1"
        },
        {
          "aa_ref": "R",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 4,
          "exon_rank_end": null,
          "exon_count": 16,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "FERMT3",
          "gene_hgnc_id": 23151,
          "hgvs_c": "c.268C>T",
          "hgvs_p": "p.Arg90Cys",
          "transcript": "NM_001382448.1",
          "protein_id": "NP_001369377.1",
          "transcript_support_level": null,
          "aa_start": 90,
          "aa_end": null,
          "aa_length": 663,
          "cds_start": 268,
          "cds_end": null,
          "cds_length": 1992,
          "cdna_start": null,
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          "mane_select": null,
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        },
        {
          "aa_ref": "R",
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          "strand": true,
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          ],
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          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "FERMT3",
          "gene_hgnc_id": 23151,
          "hgvs_c": "c.268C>T",
          "hgvs_p": "p.Arg90Cys",
          "transcript": "ENST00000544997.6",
          "protein_id": "ENSP00000445778.2",
          "transcript_support_level": 3,
          "aa_start": 90,
          "aa_end": null,
          "aa_length": 663,
          "cds_start": 268,
          "cds_end": null,
          "cds_length": 1992,
          "cdna_start": null,
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          "cdna_length": null,
          "mane_select": null,
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          "biotype": "protein_coding",
          "feature": "ENST00000544997.6"
        },
        {
          "aa_ref": "R",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 2,
          "exon_rank_end": null,
          "exon_count": 14,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "FERMT3",
          "gene_hgnc_id": 23151,
          "hgvs_c": "c.268C>T",
          "hgvs_p": "p.Arg90Cys",
          "transcript": "ENST00000698852.1",
          "protein_id": "ENSP00000513984.1",
          "transcript_support_level": null,
          "aa_start": 90,
          "aa_end": null,
          "aa_length": 663,
          "cds_start": 268,
          "cds_end": null,
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          "feature": "ENST00000698852.1"
        },
        {
          "aa_ref": "R",
          "aa_alt": "C",
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          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 15,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "FERMT3",
          "gene_hgnc_id": 23151,
          "hgvs_c": "c.268C>T",
          "hgvs_p": "p.Arg90Cys",
          "transcript": "ENST00000698861.1",
          "protein_id": "ENSP00000513989.1",
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        {
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          ],
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          "exon_count": 15,
          "intron_rank": null,
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          "gene_symbol": "FERMT3",
          "gene_hgnc_id": 23151,
          "hgvs_c": "c.268C>T",
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          "transcript": "ENST00000698863.1",
          "protein_id": "ENSP00000513991.1",
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        },
        {
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          "strand": true,
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          ],
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          "exon_count": 15,
          "intron_rank": null,
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          "gene_symbol": "FERMT3",
          "gene_hgnc_id": 23151,
          "hgvs_c": "c.268C>T",
          "hgvs_p": "p.Arg90Cys",
          "transcript": "ENST00000698870.1",
          "protein_id": "ENSP00000513996.1",
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          "cdna_start": null,
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          "cdna_length": null,
          "mane_select": null,
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          "biotype": "protein_coding",
          "feature": "ENST00000698870.1"
        },
        {
          "aa_ref": "R",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 15,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "FERMT3",
          "gene_hgnc_id": 23151,
          "hgvs_c": "c.268C>T",
          "hgvs_p": "p.Arg90Cys",
          "transcript": "ENST00000962568.1",
          "protein_id": "ENSP00000632627.1",
          "transcript_support_level": null,
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          "cds_start": 268,
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          "cdna_start": null,
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          "cdna_length": null,
          "mane_select": null,
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        {
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          "transcript": "ENST00000698875.1",
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          "biotype": "retained_intron",
          "feature": "ENST00000698875.1"
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      ],
      "gene_symbol": "FERMT3",
      "gene_hgnc_id": 23151,
      "dbsnp": "rs373315115",
      "frequency_reference_population": 0.00013629043,
      "hom_count_reference_population": 0,
      "allele_count_reference_population": 220,
      "gnomad_exomes_af": 0.000132022,
      "gnomad_genomes_af": 0.000177251,
      "gnomad_exomes_ac": 193,
      "gnomad_genomes_ac": 27,
      "gnomad_exomes_homalt": 0,
      "gnomad_genomes_homalt": 0,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": 0.10990890860557556,
      "computational_prediction_selected": "Benign",
      "computational_source_selected": "MetaRNN",
      "splice_score_selected": 0.09000000357627869,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": 0.145,
      "revel_prediction": "Benign",
      "alphamissense_score": 0.1545,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": -0.32,
      "bayesdelnoaf_prediction": "Benign",
      "phylop100way_score": 0.818,
      "phylop100way_prediction": "Benign",
      "spliceai_max_score": 0.09,
      "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": -3,
      "acmg_classification": "Likely_benign",
      "acmg_criteria": "BP4_Moderate,BS1_Supporting",
      "acmg_by_gene": [
        {
          "score": -3,
          "benign_score": 3,
          "pathogenic_score": 0,
          "criteria": [
            "BP4_Moderate",
            "BS1_Supporting"
          ],
          "verdict": "Likely_benign",
          "transcript": "NM_001382364.1",
          "gene_symbol": "FERMT3",
          "hgnc_id": 23151,
          "effects": [
            "5_prime_UTR_premature_start_codon_gain_variant"
          ],
          "inheritance_mode": "AR",
          "hgvs_c": "c.-273C>T",
          "hgvs_p": null
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      ],
      "clinvar_disease": "Inborn genetic diseases,Leukocyte adhesion deficiency 3",
      "clinvar_classification": "Uncertain significance",
      "clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
      "clinvar_submissions_summary": "US:2",
      "phenotype_combined": "Leukocyte adhesion deficiency 3|Inborn genetic diseases",
      "pathogenicity_classification_combined": "Uncertain significance",
      "custom_annotations": null
    }
  ],
  "message": null
}