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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: X-103500389-A-C (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=103500389&ref=A&alt=C&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "X",
      "pos": 103500389,
      "ref": "A",
      "alt": "C",
      "effect": "missense_variant",
      "transcript": "NM_080879.3",
      "consequences": [
        {
          "aa_ref": "L",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 3,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RAB40A",
          "gene_hgnc_id": 18283,
          "hgvs_c": "c.368T>G",
          "hgvs_p": "p.Leu123Arg",
          "transcript": "NM_080879.3",
          "protein_id": "NP_543155.2",
          "transcript_support_level": null,
          "aa_start": 123,
          "aa_end": null,
          "aa_length": 277,
          "cds_start": 368,
          "cds_end": null,
          "cds_length": 834,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": "ENST00000304236.2",
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_080879.3"
        },
        {
          "aa_ref": "L",
          "aa_alt": "R",
          "canonical": true,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 3,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RAB40A",
          "gene_hgnc_id": 18283,
          "hgvs_c": "c.368T>G",
          "hgvs_p": "p.Leu123Arg",
          "transcript": "ENST00000304236.2",
          "protein_id": "ENSP00000305648.1",
          "transcript_support_level": 2,
          "aa_start": 123,
          "aa_end": null,
          "aa_length": 277,
          "cds_start": 368,
          "cds_end": null,
          "cds_length": 834,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": "NM_080879.3",
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000304236.2"
        },
        {
          "aa_ref": "L",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 1,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RAB40A",
          "gene_hgnc_id": 18283,
          "hgvs_c": "c.368T>G",
          "hgvs_p": "p.Leu123Arg",
          "transcript": "ENST00000372633.1",
          "protein_id": "ENSP00000361716.1",
          "transcript_support_level": 6,
          "aa_start": 123,
          "aa_end": null,
          "aa_length": 277,
          "cds_start": 368,
          "cds_end": null,
          "cds_length": 834,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000372633.1"
        },
        {
          "aa_ref": "L",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 4,
          "exon_rank_end": null,
          "exon_count": 4,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RAB40A",
          "gene_hgnc_id": 18283,
          "hgvs_c": "c.368T>G",
          "hgvs_p": "p.Leu123Arg",
          "transcript": "ENST00000905301.1",
          "protein_id": "ENSP00000575360.1",
          "transcript_support_level": null,
          "aa_start": 123,
          "aa_end": null,
          "aa_length": 277,
          "cds_start": 368,
          "cds_end": null,
          "cds_length": 834,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000905301.1"
        },
        {
          "aa_ref": "L",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 2,
          "exon_rank_end": null,
          "exon_count": 2,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RAB40A",
          "gene_hgnc_id": 18283,
          "hgvs_c": "c.368T>G",
          "hgvs_p": "p.Leu123Arg",
          "transcript": "ENST00000905302.1",
          "protein_id": "ENSP00000575361.1",
          "transcript_support_level": null,
          "aa_start": 123,
          "aa_end": null,
          "aa_length": 277,
          "cds_start": 368,
          "cds_end": null,
          "cds_length": 834,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000905302.1"
        },
        {
          "aa_ref": "L",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 2,
          "exon_rank_end": null,
          "exon_count": 2,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RAB40A",
          "gene_hgnc_id": 18283,
          "hgvs_c": "c.368T>G",
          "hgvs_p": "p.Leu123Arg",
          "transcript": "ENST00000942559.1",
          "protein_id": "ENSP00000612618.1",
          "transcript_support_level": null,
          "aa_start": 123,
          "aa_end": null,
          "aa_length": 277,
          "cds_start": 368,
          "cds_end": null,
          "cds_length": 834,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000942559.1"
        },
        {
          "aa_ref": "L",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 2,
          "exon_rank_end": null,
          "exon_count": 2,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RAB40A",
          "gene_hgnc_id": 18283,
          "hgvs_c": "c.368T>G",
          "hgvs_p": "p.Leu123Arg",
          "transcript": "ENST00000942560.1",
          "protein_id": "ENSP00000612619.1",
          "transcript_support_level": null,
          "aa_start": 123,
          "aa_end": null,
          "aa_length": 277,
          "cds_start": 368,
          "cds_end": null,
          "cds_length": 834,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000942560.1"
        },
        {
          "aa_ref": "L",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 2,
          "exon_rank_end": null,
          "exon_count": 2,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RAB40A",
          "gene_hgnc_id": 18283,
          "hgvs_c": "c.368T>G",
          "hgvs_p": "p.Leu123Arg",
          "transcript": "XM_047441843.1",
          "protein_id": "XP_047297799.1",
          "transcript_support_level": null,
          "aa_start": 123,
          "aa_end": null,
          "aa_length": 277,
          "cds_start": 368,
          "cds_end": null,
          "cds_length": 834,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "XM_047441843.1"
        },
        {
          "aa_ref": "L",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 2,
          "exon_rank_end": null,
          "exon_count": 2,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RAB40A",
          "gene_hgnc_id": 18283,
          "hgvs_c": "c.368T>G",
          "hgvs_p": "p.Leu123Arg",
          "transcript": "XM_047441844.1",
          "protein_id": "XP_047297800.1",
          "transcript_support_level": null,
          "aa_start": 123,
          "aa_end": null,
          "aa_length": 277,
          "cds_start": 368,
          "cds_end": null,
          "cds_length": 834,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "XM_047441844.1"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 9,
          "exon_rank_end": null,
          "exon_count": 9,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "LL0XNC01-250H12.3",
          "gene_hgnc_id": null,
          "hgvs_c": "n.1882A>C",
          "hgvs_p": null,
          "transcript": "ENST00000445990.2",
          "protein_id": null,
          "transcript_support_level": 3,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": null,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "pseudogene",
          "feature": "ENST00000445990.2"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 9,
          "exon_rank_end": null,
          "exon_count": 9,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "LL0XNC01-250H12.3",
          "gene_hgnc_id": null,
          "hgvs_c": "n.1917A>C",
          "hgvs_p": null,
          "transcript": "ENST00000801275.1",
          "protein_id": null,
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": null,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "pseudogene",
          "feature": "ENST00000801275.1"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 8,
          "exon_rank_end": null,
          "exon_count": 8,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "LL0XNC01-250H12.3",
          "gene_hgnc_id": null,
          "hgvs_c": "n.1878A>C",
          "hgvs_p": null,
          "transcript": "ENST00000801276.1",
          "protein_id": null,
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": null,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "pseudogene",
          "feature": "ENST00000801276.1"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 9,
          "exon_rank_end": null,
          "exon_count": 9,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "LL0XNC01-250H12.3",
          "gene_hgnc_id": null,
          "hgvs_c": "n.1821A>C",
          "hgvs_p": null,
          "transcript": "ENST00000801277.1",
          "protein_id": null,
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": null,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "pseudogene",
          "feature": "ENST00000801277.1"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 7,
          "exon_rank_end": null,
          "exon_count": 7,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "LL0XNC01-250H12.3",
          "gene_hgnc_id": null,
          "hgvs_c": "n.1337A>C",
          "hgvs_p": null,
          "transcript": "ENST00000801278.1",
          "protein_id": null,
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": null,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "pseudogene",
          "feature": "ENST00000801278.1"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 9,
          "exon_rank_end": null,
          "exon_count": 9,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "LL0XNC01-250H12.3",
          "gene_hgnc_id": null,
          "hgvs_c": "n.2059A>C",
          "hgvs_p": null,
          "transcript": "NR_188433.1",
          "protein_id": null,
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": null,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "pseudogene",
          "feature": "NR_188433.1"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 9,
          "exon_rank_end": null,
          "exon_count": 9,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "LL0XNC01-250H12.3",
          "gene_hgnc_id": null,
          "hgvs_c": "n.1986A>C",
          "hgvs_p": null,
          "transcript": "NR_188435.1",
          "protein_id": null,
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": null,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "pseudogene",
          "feature": "NR_188435.1"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 8,
          "exon_rank_end": null,
          "exon_count": 8,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "LL0XNC01-250H12.3",
          "gene_hgnc_id": null,
          "hgvs_c": "n.1783A>C",
          "hgvs_p": null,
          "transcript": "NR_188436.1",
          "protein_id": null,
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": null,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "pseudogene",
          "feature": "NR_188436.1"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 9,
          "exon_rank_end": null,
          "exon_count": 9,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "LL0XNC01-250H12.3",
          "gene_hgnc_id": null,
          "hgvs_c": "n.1862A>C",
          "hgvs_p": null,
          "transcript": "NR_188437.1",
          "protein_id": null,
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": null,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "pseudogene",
          "feature": "NR_188437.1"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 8,
          "exon_rank_end": null,
          "exon_count": 8,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "LL0XNC01-250H12.3",
          "gene_hgnc_id": null,
          "hgvs_c": "n.1710A>C",
          "hgvs_p": null,
          "transcript": "NR_188438.1",
          "protein_id": null,
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": null,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "pseudogene",
          "feature": "NR_188438.1"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 6,
          "intron_rank": 5,
          "intron_rank_end": null,
          "gene_symbol": "LL0XNC01-250H12.3",
          "gene_hgnc_id": null,
          "hgvs_c": "n.843-17259A>C",
          "hgvs_p": null,
          "transcript": "ENST00000628546.2",
          "protein_id": null,
          "transcript_support_level": 5,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": null,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "pseudogene",
          "feature": "ENST00000628546.2"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
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      "gnomad_exomes_homalt": null,
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      "computational_score_selected": 0.9578031301498413,
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      "computational_source_selected": "MetaRNN",
      "splice_score_selected": 0,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
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      "revel_prediction": "Pathogenic",
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      "bayesdelnoaf_score": 0.55,
      "bayesdelnoaf_prediction": "Pathogenic",
      "phylop100way_score": 6.523,
      "phylop100way_prediction": "Uncertain_significance",
      "spliceai_max_score": 0,
      "spliceai_max_prediction": "Benign",
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      "acmg_score": 6,
      "acmg_classification": "Likely_pathogenic",
      "acmg_criteria": "PM2,PP3_Strong",
      "acmg_by_gene": [
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          "benign_score": 0,
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            "PP3_Strong"
          ],
          "verdict": "Likely_pathogenic",
          "transcript": "NM_080879.3",
          "gene_symbol": "RAB40A",
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          "effects": [
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          ],
          "inheritance_mode": "",
          "hgvs_c": "c.368T>G",
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        {
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            "PP3_Strong"
          ],
          "verdict": "Likely_pathogenic",
          "transcript": "ENST00000445990.2",
          "gene_symbol": "LL0XNC01-250H12.3",
          "hgnc_id": null,
          "effects": [
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          ],
          "inheritance_mode": "",
          "hgvs_c": "n.1882A>C",
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      ],
      "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
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  ],
  "message": null
}