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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: 1-197617713-T-A (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=197617713&ref=T&alt=A&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "1",
      "pos": 197617713,
      "ref": "T",
      "alt": "A",
      "effect": "missense_variant",
      "transcript": "NM_001195215.2",
      "consequences": [
        {
          "aa_ref": "Y",
          "aa_alt": "F",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 11,
          "exon_rank_end": null,
          "exon_count": 23,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "DENND1B",
          "gene_hgnc_id": 28404,
          "hgvs_c": "c.719A>T",
          "hgvs_p": "p.Tyr240Phe",
          "transcript": "NM_001195215.2",
          "protein_id": "NP_001182144.1",
          "transcript_support_level": null,
          "aa_start": 240,
          "aa_end": null,
          "aa_length": 775,
          "cds_start": 719,
          "cds_end": null,
          "cds_length": 2328,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": "ENST00000620048.6",
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_001195215.2"
        },
        {
          "aa_ref": "Y",
          "aa_alt": "F",
          "canonical": true,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 11,
          "exon_rank_end": null,
          "exon_count": 23,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "DENND1B",
          "gene_hgnc_id": 28404,
          "hgvs_c": "c.719A>T",
          "hgvs_p": "p.Tyr240Phe",
          "transcript": "ENST00000620048.6",
          "protein_id": "ENSP00000479816.1",
          "transcript_support_level": 5,
          "aa_start": 240,
          "aa_end": null,
          "aa_length": 775,
          "cds_start": 719,
          "cds_end": null,
          "cds_length": 2328,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": "NM_001195215.2",
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000620048.6"
        },
        {
          "aa_ref": "Y",
          "aa_alt": "F",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 11,
          "exon_rank_end": null,
          "exon_count": 16,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "DENND1B",
          "gene_hgnc_id": 28404,
          "hgvs_c": "c.719A>T",
          "hgvs_p": "p.Tyr240Phe",
          "transcript": "ENST00000367396.7",
          "protein_id": "ENSP00000356366.3",
          "transcript_support_level": 1,
          "aa_start": 240,
          "aa_end": null,
          "aa_length": 426,
          "cds_start": 719,
          "cds_end": null,
          "cds_length": 1281,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000367396.7"
        },
        {
          "aa_ref": "Y",
          "aa_alt": "F",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 11,
          "exon_rank_end": null,
          "exon_count": 16,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "DENND1B",
          "gene_hgnc_id": 28404,
          "hgvs_c": "c.629A>T",
          "hgvs_p": "p.Tyr210Phe",
          "transcript": "ENST00000235453.8",
          "protein_id": "ENSP00000235453.4",
          "transcript_support_level": 1,
          "aa_start": 210,
          "aa_end": null,
          "aa_length": 396,
          "cds_start": 629,
          "cds_end": null,
          "cds_length": 1191,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000235453.8"
        },
        {
          "aa_ref": "Y",
          "aa_alt": "F",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 10,
          "exon_rank_end": null,
          "exon_count": 22,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "DENND1B",
          "gene_hgnc_id": 28404,
          "hgvs_c": "c.665A>T",
          "hgvs_p": "p.Tyr222Phe",
          "transcript": "ENST00000887109.1",
          "protein_id": "ENSP00000557168.1",
          "transcript_support_level": null,
          "aa_start": 222,
          "aa_end": null,
          "aa_length": 757,
          "cds_start": 665,
          "cds_end": null,
          "cds_length": 2274,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000887109.1"
        },
        {
          "aa_ref": "Y",
          "aa_alt": "F",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 10,
          "exon_rank_end": null,
          "exon_count": 22,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "DENND1B",
          "gene_hgnc_id": 28404,
          "hgvs_c": "c.659A>T",
          "hgvs_p": "p.Tyr220Phe",
          "transcript": "ENST00000887105.1",
          "protein_id": "ENSP00000557164.1",
          "transcript_support_level": null,
          "aa_start": 220,
          "aa_end": null,
          "aa_length": 755,
          "cds_start": 659,
          "cds_end": null,
          "cds_length": 2268,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000887105.1"
        },
        {
          "aa_ref": "Y",
          "aa_alt": "F",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 9,
          "exon_rank_end": null,
          "exon_count": 21,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "DENND1B",
          "gene_hgnc_id": 28404,
          "hgvs_c": "c.605A>T",
          "hgvs_p": "p.Tyr202Phe",
          "transcript": "ENST00000887107.1",
          "protein_id": "ENSP00000557166.1",
          "transcript_support_level": null,
          "aa_start": 202,
          "aa_end": null,
          "aa_length": 737,
          "cds_start": 605,
          "cds_end": null,
          "cds_length": 2214,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000887107.1"
        },
        {
          "aa_ref": "Y",
          "aa_alt": "F",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 11,
          "exon_rank_end": null,
          "exon_count": 22,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "DENND1B",
          "gene_hgnc_id": 28404,
          "hgvs_c": "c.719A>T",
          "hgvs_p": "p.Tyr240Phe",
          "transcript": "ENST00000887108.1",
          "protein_id": "ENSP00000557167.1",
          "transcript_support_level": null,
          "aa_start": 240,
          "aa_end": null,
          "aa_length": 733,
          "cds_start": 719,
          "cds_end": null,
          "cds_length": 2202,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000887108.1"
        },
        {
          "aa_ref": "Y",
          "aa_alt": "F",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 10,
          "exon_rank_end": null,
          "exon_count": 21,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "DENND1B",
          "gene_hgnc_id": 28404,
          "hgvs_c": "c.659A>T",
          "hgvs_p": "p.Tyr220Phe",
          "transcript": "ENST00000887111.1",
          "protein_id": "ENSP00000557170.1",
          "transcript_support_level": null,
          "aa_start": 220,
          "aa_end": null,
          "aa_length": 713,
          "cds_start": 659,
          "cds_end": null,
          "cds_length": 2142,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000887111.1"
        },
        {
          "aa_ref": "Y",
          "aa_alt": "F",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 8,
          "exon_rank_end": null,
          "exon_count": 20,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "DENND1B",
          "gene_hgnc_id": 28404,
          "hgvs_c": "c.494A>T",
          "hgvs_p": "p.Tyr165Phe",
          "transcript": "ENST00000887110.1",
          "protein_id": "ENSP00000557169.1",
          "transcript_support_level": null,
          "aa_start": 165,
          "aa_end": null,
          "aa_length": 700,
          "cds_start": 494,
          "cds_end": null,
          "cds_length": 2103,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000887110.1"
        },
        {
          "aa_ref": "Y",
          "aa_alt": "F",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 11,
          "exon_rank_end": null,
          "exon_count": 16,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "DENND1B",
          "gene_hgnc_id": 28404,
          "hgvs_c": "c.719A>T",
          "hgvs_p": "p.Tyr240Phe",
          "transcript": "NM_144977.5",
          "protein_id": "NP_659414.2",
          "transcript_support_level": null,
          "aa_start": 240,
          "aa_end": null,
          "aa_length": 426,
          "cds_start": 719,
          "cds_end": null,
          "cds_length": 1281,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_144977.5"
        },
        {
          "aa_ref": "Y",
          "aa_alt": "F",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 11,
          "exon_rank_end": null,
          "exon_count": 16,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "DENND1B",
          "gene_hgnc_id": 28404,
          "hgvs_c": "c.629A>T",
          "hgvs_p": "p.Tyr210Phe",
          "transcript": "NM_001300858.2",
          "protein_id": "NP_001287787.1",
          "transcript_support_level": null,
          "aa_start": 210,
          "aa_end": null,
          "aa_length": 396,
          "cds_start": 629,
          "cds_end": null,
          "cds_length": 1191,
          "cdna_start": null,
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          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_001300858.2"
        },
        {
          "aa_ref": "Y",
          "aa_alt": "F",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 11,
          "exon_rank_end": null,
          "exon_count": 23,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "DENND1B",
          "gene_hgnc_id": 28404,
          "hgvs_c": "c.863A>T",
          "hgvs_p": "p.Tyr288Phe",
          "transcript": "XM_011509246.3",
          "protein_id": "XP_011507548.1",
          "transcript_support_level": null,
          "aa_start": 288,
          "aa_end": null,
          "aa_length": 823,
          "cds_start": 863,
          "cds_end": null,
          "cds_length": 2472,
          "cdna_start": null,
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          "cdna_length": null,
          "mane_select": null,
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          "biotype": "protein_coding",
          "feature": "XM_011509246.3"
        },
        {
          "aa_ref": "Y",
          "aa_alt": "F",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 10,
          "exon_rank_end": null,
          "exon_count": 22,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "DENND1B",
          "gene_hgnc_id": 28404,
          "hgvs_c": "c.803A>T",
          "hgvs_p": "p.Tyr268Phe",
          "transcript": "XM_011509247.2",
          "protein_id": "XP_011507549.1",
          "transcript_support_level": null,
          "aa_start": 268,
          "aa_end": null,
          "aa_length": 803,
          "cds_start": 803,
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        {
          "aa_ref": "Y",
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          ],
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          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "DENND1B",
          "gene_hgnc_id": 28404,
          "hgvs_c": "c.758A>T",
          "hgvs_p": "p.Tyr253Phe",
          "transcript": "XM_011509248.3",
          "protein_id": "XP_011507550.1",
          "transcript_support_level": null,
          "aa_start": 253,
          "aa_end": null,
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          "cds_start": 758,
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          "cds_length": 2367,
          "cdna_start": null,
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          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "XM_011509248.3"
        },
        {
          "aa_ref": "Y",
          "aa_alt": "F",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 12,
          "exon_rank_end": null,
          "exon_count": 24,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "DENND1B",
          "gene_hgnc_id": 28404,
          "hgvs_c": "c.689A>T",
          "hgvs_p": "p.Tyr230Phe",
          "transcript": "XM_011509249.3",
          "protein_id": "XP_011507551.1",
          "transcript_support_level": null,
          "aa_start": 230,
          "aa_end": null,
          "aa_length": 765,
          "cds_start": 689,
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          "biotype": "protein_coding",
          "feature": "XM_011509249.3"
        },
        {
          "aa_ref": "Y",
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          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 10,
          "exon_rank_end": null,
          "exon_count": 22,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "DENND1B",
          "gene_hgnc_id": 28404,
          "hgvs_c": "c.659A>T",
          "hgvs_p": "p.Tyr220Phe",
          "transcript": "XM_005244931.3",
          "protein_id": "XP_005244988.1",
          "transcript_support_level": null,
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          "cds_start": 659,
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        },
        {
          "aa_ref": "Y",
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          "strand": false,
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          ],
          "exon_rank": 9,
          "exon_rank_end": null,
          "exon_count": 21,
          "intron_rank": null,
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          "gene_symbol": "DENND1B",
          "gene_hgnc_id": 28404,
          "hgvs_c": "c.629A>T",
          "hgvs_p": "p.Tyr210Phe",
          "transcript": "XM_047447700.1",
          "protein_id": "XP_047303656.1",
          "transcript_support_level": null,
          "aa_start": 210,
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          "cds_length": 2238,
          "cdna_start": null,
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          "biotype": "protein_coding",
          "feature": "XM_047447700.1"
        },
        {
          "aa_ref": "Y",
          "aa_alt": "F",
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          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 10,
          "exon_rank_end": null,
          "exon_count": 22,
          "intron_rank": null,
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          "gene_symbol": "DENND1B",
          "gene_hgnc_id": 28404,
          "hgvs_c": "c.116A>T",
          "hgvs_p": "p.Tyr39Phe",
          "transcript": "XM_024453626.2",
          "protein_id": "XP_024309394.1",
          "transcript_support_level": null,
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          "aa_end": null,
          "aa_length": 574,
          "cds_start": 116,
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          "cds_length": 1725,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "XM_024453626.2"
        },
        {
          "aa_ref": "Y",
          "aa_alt": "F",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 11,
          "exon_rank_end": null,
          "exon_count": 23,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "DENND1B",
          "gene_hgnc_id": 28404,
          "hgvs_c": "c.116A>T",
          "hgvs_p": "p.Tyr39Phe",
          "transcript": "XM_047447711.1",
          "protein_id": "XP_047303667.1",
          "transcript_support_level": null,
          "aa_start": 39,
          "aa_end": null,
          "aa_length": 574,
          "cds_start": 116,
          "cds_end": null,
          "cds_length": 1725,
          "cdna_start": null,
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        {
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          "transcript": "NR_125340.2",
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          "biotype": "pseudogene",
          "feature": "NR_125340.2"
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      ],
      "gene_symbol": "DENND1B",
      "gene_hgnc_id": 28404,
      "dbsnp": "rs371820117",
      "frequency_reference_population": 0.00033340382,
      "hom_count_reference_population": 0,
      "allele_count_reference_population": 536,
      "gnomad_exomes_af": 0.000350155,
      "gnomad_genomes_af": 0.000171999,
      "gnomad_exomes_ac": 510,
      "gnomad_genomes_ac": 26,
      "gnomad_exomes_homalt": 0,
      "gnomad_genomes_homalt": 0,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": 0.1514550745487213,
      "computational_prediction_selected": "Benign",
      "computational_source_selected": "MetaRNN",
      "splice_score_selected": 0.009999999776482582,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": 0.065,
      "revel_prediction": "Benign",
      "alphamissense_score": 0.0698,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": -0.58,
      "bayesdelnoaf_prediction": "Benign",
      "phylop100way_score": 3.94,
      "phylop100way_prediction": "Uncertain_significance",
      "spliceai_max_score": 0.01,
      "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": "Likely_benign",
      "acmg_criteria": "BP4_Moderate",
      "acmg_by_gene": [
        {
          "score": -2,
          "benign_score": 2,
          "pathogenic_score": 0,
          "criteria": [
            "BP4_Moderate"
          ],
          "verdict": "Likely_benign",
          "transcript": "NM_001195215.2",
          "gene_symbol": "DENND1B",
          "hgnc_id": 28404,
          "effects": [
            "missense_variant"
          ],
          "inheritance_mode": "AR",
          "hgvs_c": "c.719A>T",
          "hgvs_p": "p.Tyr240Phe"
        }
      ],
      "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
}