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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: 1-12009641-C-T (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=12009641&ref=C&alt=T&genome=hg38&allGenes=true"

API Response

json
{
  "message": null,
  "variants": [
    {
      "acmg_by_gene": [
        {
          "benign_score": 1,
          "criteria": [
            "PS3",
            "PM5",
            "PP2",
            "PP3",
            "PP5_Very_Strong",
            "BS1_Supporting"
          ],
          "effects": [
            "missense_variant"
          ],
          "gene_symbol": "MFN2",
          "hgnc_id": 16877,
          "hgvs_c": "c.2119C>T",
          "hgvs_p": "p.Arg707Trp",
          "inheritance_mode": "AR,AD,SD",
          "pathogenic_score": 16,
          "score": 15,
          "transcript": "NM_014874.4",
          "verdict": "Pathogenic"
        }
      ],
      "acmg_classification": "Pathogenic",
      "acmg_criteria": "PS3,PM5,PP2,PP3,PP5_Very_Strong,BS1_Supporting",
      "acmg_score": 15,
      "allele_count_reference_population": 731,
      "alphamissense_prediction": null,
      "alphamissense_score": 0.3702,
      "alt": "T",
      "apogee2_prediction": null,
      "apogee2_score": null,
      "bayesdelnoaf_prediction": "Pathogenic",
      "bayesdelnoaf_score": 0.41,
      "chr": "1",
      "clinvar_classification": "Pathogenic/Likely pathogenic",
      "clinvar_disease": " autosomal recessive, axonal, hereditary motor and sensory, type 2A, type 2a2b, type 6A,Charcot-Marie-Tooth disease,Charcot-Marie-Tooth disease type 2,Charcot-Marie-Tooth disease type 2A2,Hereditary motor and sensory neuropathy with optic atrophy,Inborn genetic diseases,MFN2-related disorder,Multiple symmetric lipomatosis,Neuropathy,Peripheral axonal neuropathy,Tip-toe gait,not provided",
      "clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
      "clinvar_submissions_summary": "P:17 LP:5 O:2",
      "computational_prediction_selected": "Pathogenic",
      "computational_score_selected": 0.8352029919624329,
      "computational_source_selected": "MetaRNN",
      "consequences": [
        {
          "aa_alt": "W",
          "aa_end": null,
          "aa_length": 757,
          "aa_ref": "R",
          "aa_start": 707,
          "biotype": "protein_coding",
          "canonical": false,
          "cdna_end": null,
          "cdna_length": 4407,
          "cdna_start": 2309,
          "cds_end": null,
          "cds_length": 2274,
          "cds_start": 2119,
          "consequences": [
            "missense_variant"
          ],
          "exon_count": 19,
          "exon_rank": 18,
          "exon_rank_end": null,
          "feature": "NM_014874.4",
          "gene_hgnc_id": 16877,
          "gene_symbol": "MFN2",
          "hgvs_c": "c.2119C>T",
          "hgvs_p": "p.Arg707Trp",
          "intron_rank": null,
          "intron_rank_end": null,
          "mane_plus": null,
          "mane_select": "ENST00000235329.10",
          "protein_coding": true,
          "protein_id": "NP_055689.1",
          "strand": true,
          "transcript": "NM_014874.4",
          "transcript_support_level": null
        },
        {
          "aa_alt": "W",
          "aa_end": null,
          "aa_length": 757,
          "aa_ref": "R",
          "aa_start": 707,
          "biotype": "protein_coding",
          "canonical": true,
          "cdna_end": null,
          "cdna_length": 4407,
          "cdna_start": 2309,
          "cds_end": null,
          "cds_length": 2274,
          "cds_start": 2119,
          "consequences": [
            "missense_variant"
          ],
          "exon_count": 19,
          "exon_rank": 18,
          "exon_rank_end": null,
          "feature": "ENST00000235329.10",
          "gene_hgnc_id": 16877,
          "gene_symbol": "MFN2",
          "hgvs_c": "c.2119C>T",
          "hgvs_p": "p.Arg707Trp",
          "intron_rank": null,
          "intron_rank_end": null,
          "mane_plus": null,
          "mane_select": "NM_014874.4",
          "protein_coding": true,
          "protein_id": "ENSP00000235329.5",
          "strand": true,
          "transcript": "ENST00000235329.10",
          "transcript_support_level": 1
        },
        {
          "aa_alt": "W",
          "aa_end": null,
          "aa_length": 808,
          "aa_ref": "R",
          "aa_start": 707,
          "biotype": "protein_coding",
          "canonical": false,
          "cdna_end": null,
          "cdna_length": 3584,
          "cdna_start": 2544,
          "cds_end": null,
          "cds_length": 2427,
          "cds_start": 2119,
          "consequences": [
            "missense_variant"
          ],
          "exon_count": 19,
          "exon_rank": 18,
          "exon_rank_end": null,
          "feature": "ENST00000675298.1",
          "gene_hgnc_id": 16877,
          "gene_symbol": "MFN2",
          "hgvs_c": "c.2119C>T",
          "hgvs_p": "p.Arg707Trp",
          "intron_rank": null,
          "intron_rank_end": null,
          "mane_plus": null,
          "mane_select": null,
          "protein_coding": true,
          "protein_id": "ENSP00000501839.1",
          "strand": true,
          "transcript": "ENST00000675298.1",
          "transcript_support_level": null
        },
        {
          "aa_alt": "W",
          "aa_end": null,
          "aa_length": 801,
          "aa_ref": "R",
          "aa_start": 751,
          "biotype": "protein_coding",
          "canonical": false,
          "cdna_end": null,
          "cdna_length": 4766,
          "cdna_start": 2676,
          "cds_end": null,
          "cds_length": 2406,
          "cds_start": 2251,
          "consequences": [
            "missense_variant"
          ],
          "exon_count": 20,
          "exon_rank": 19,
          "exon_rank_end": null,
          "feature": "ENST00000675817.1",
          "gene_hgnc_id": 16877,
          "gene_symbol": "MFN2",
          "hgvs_c": "c.2251C>T",
          "hgvs_p": "p.Arg751Trp",
          "intron_rank": null,
          "intron_rank_end": null,
          "mane_plus": null,
          "mane_select": null,
          "protein_coding": true,
          "protein_id": "ENSP00000502422.1",
          "strand": true,
          "transcript": "ENST00000675817.1",
          "transcript_support_level": null
        },
        {
          "aa_alt": "W",
          "aa_end": null,
          "aa_length": 801,
          "aa_ref": "R",
          "aa_start": 751,
          "biotype": "protein_coding",
          "canonical": false,
          "cdna_end": null,
          "cdna_length": 4623,
          "cdna_start": 2534,
          "cds_end": null,
          "cds_length": 2406,
          "cds_start": 2251,
          "consequences": [
            "missense_variant"
          ],
          "exon_count": 21,
          "exon_rank": 20,
          "exon_rank_end": null,
          "feature": "ENST00000898895.1",
          "gene_hgnc_id": 16877,
          "gene_symbol": "MFN2",
          "hgvs_c": "c.2251C>T",
          "hgvs_p": "p.Arg751Trp",
          "intron_rank": null,
          "intron_rank_end": null,
          "mane_plus": null,
          "mane_select": null,
          "protein_coding": true,
          "protein_id": "ENSP00000568954.1",
          "strand": true,
          "transcript": "ENST00000898895.1",
          "transcript_support_level": null
        },
        {
          "aa_alt": "W",
          "aa_end": null,
          "aa_length": 801,
          "aa_ref": "R",
          "aa_start": 751,
          "biotype": "protein_coding",
          "canonical": false,
          "cdna_end": null,
          "cdna_length": 4521,
          "cdna_start": 2425,
          "cds_end": null,
          "cds_length": 2406,
          "cds_start": 2251,
          "consequences": [
            "missense_variant"
          ],
          "exon_count": 21,
          "exon_rank": 20,
          "exon_rank_end": null,
          "feature": "ENST00000967404.1",
          "gene_hgnc_id": 16877,
          "gene_symbol": "MFN2",
          "hgvs_c": "c.2251C>T",
          "hgvs_p": "p.Arg751Trp",
          "intron_rank": null,
          "intron_rank_end": null,
          "mane_plus": null,
          "mane_select": null,
          "protein_coding": true,
          "protein_id": "ENSP00000637463.1",
          "strand": true,
          "transcript": "ENST00000967404.1",
          "transcript_support_level": null
        },
        {
          "aa_alt": "W",
          "aa_end": null,
          "aa_length": 801,
          "aa_ref": "R",
          "aa_start": 751,
          "biotype": "protein_coding",
          "canonical": false,
          "cdna_end": null,
          "cdna_length": 2786,
          "cdna_start": 2505,
          "cds_end": null,
          "cds_length": 2406,
          "cds_start": 2251,
          "consequences": [
            "missense_variant"
          ],
          "exon_count": 20,
          "exon_rank": 19,
          "exon_rank_end": null,
          "feature": "ENST00000967417.1",
          "gene_hgnc_id": 16877,
          "gene_symbol": "MFN2",
          "hgvs_c": "c.2251C>T",
          "hgvs_p": "p.Arg751Trp",
          "intron_rank": null,
          "intron_rank_end": null,
          "mane_plus": null,
          "mane_select": null,
          "protein_coding": true,
          "protein_id": "ENSP00000637476.1",
          "strand": true,
          "transcript": "ENST00000967417.1",
          "transcript_support_level": null
        },
        {
          "aa_alt": "W",
          "aa_end": null,
          "aa_length": 787,
          "aa_ref": "R",
          "aa_start": 737,
          "biotype": "protein_coding",
          "canonical": false,
          "cdna_end": null,
          "cdna_length": 4684,
          "cdna_start": 2586,
          "cds_end": null,
          "cds_length": 2364,
          "cds_start": 2209,
          "consequences": [
            "missense_variant"
          ],
          "exon_count": 20,
          "exon_rank": 19,
          "exon_rank_end": null,
          "feature": "ENST00000898885.1",
          "gene_hgnc_id": 16877,
          "gene_symbol": "MFN2",
          "hgvs_c": "c.2209C>T",
          "hgvs_p": "p.Arg737Trp",
          "intron_rank": null,
          "intron_rank_end": null,
          "mane_plus": null,
          "mane_select": null,
          "protein_coding": true,
          "protein_id": "ENSP00000568944.1",
          "strand": true,
          "transcript": "ENST00000898885.1",
          "transcript_support_level": null
        },
        {
          "aa_alt": "W",
          "aa_end": null,
          "aa_length": 757,
          "aa_ref": "R",
          "aa_start": 707,
          "biotype": "protein_coding",
          "canonical": false,
          "cdna_end": null,
          "cdna_length": 4262,
          "cdna_start": 2164,
          "cds_end": null,
          "cds_length": 2274,
          "cds_start": 2119,
          "consequences": [
            "missense_variant"
          ],
          "exon_count": 18,
          "exon_rank": 17,
          "exon_rank_end": null,
          "feature": "NM_001127660.2",
          "gene_hgnc_id": 16877,
          "gene_symbol": "MFN2",
          "hgvs_c": "c.2119C>T",
          "hgvs_p": "p.Arg707Trp",
          "intron_rank": null,
          "intron_rank_end": null,
          "mane_plus": null,
          "mane_select": null,
          "protein_coding": true,
          "protein_id": "NP_001121132.1",
          "strand": true,
          "transcript": "NM_001127660.2",
          "transcript_support_level": null
        },
        {
          "aa_alt": "W",
          "aa_end": null,
          "aa_length": 757,
          "aa_ref": "R",
          "aa_start": 707,
          "biotype": "protein_coding",
          "canonical": false,
          "cdna_end": null,
          "cdna_length": 4531,
          "cdna_start": 2427,
          "cds_end": null,
          "cds_length": 2274,
          "cds_start": 2119,
          "consequences": [
            "missense_variant"
          ],
          "exon_count": 18,
          "exon_rank": 17,
          "exon_rank_end": null,
          "feature": "ENST00000444836.5",
          "gene_hgnc_id": 16877,
          "gene_symbol": "MFN2",
          "hgvs_c": "c.2119C>T",
          "hgvs_p": "p.Arg707Trp",
          "intron_rank": null,
          "intron_rank_end": null,
          "mane_plus": null,
          "mane_select": null,
          "protein_coding": true,
          "protein_id": "ENSP00000416338.1",
          "strand": true,
          "transcript": "ENST00000444836.5",
          "transcript_support_level": 2
        },
        {
          "aa_alt": "W",
          "aa_end": null,
          "aa_length": 757,
          "aa_ref": "R",
          "aa_start": 707,
          "biotype": "protein_coding",
          "canonical": false,
          "cdna_end": null,
          "cdna_length": 4572,
          "cdna_start": 2482,
          "cds_end": null,
          "cds_length": 2274,
          "cds_start": 2119,
          "consequences": [
            "missense_variant"
          ],
          "exon_count": 19,
          "exon_rank": 18,
          "exon_rank_end": null,
          "feature": "ENST00000674548.1",
          "gene_hgnc_id": 16877,
          "gene_symbol": "MFN2",
          "hgvs_c": "c.2119C>T",
          "hgvs_p": "p.Arg707Trp",
          "intron_rank": null,
          "intron_rank_end": null,
          "mane_plus": null,
          "mane_select": null,
          "protein_coding": true,
          "protein_id": "ENSP00000502185.1",
          "strand": true,
          "transcript": "ENST00000674548.1",
          "transcript_support_level": null
        },
        {
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          "aa_length": 757,
          "aa_ref": "R",
          "aa_start": 707,
          "biotype": "protein_coding",
          "canonical": false,
          "cdna_end": null,
          "cdna_length": 4514,
          "cdna_start": 2419,
          "cds_end": null,
          "cds_length": 2274,
          "cds_start": 2119,
          "consequences": [
            "missense_variant"
          ],
          "exon_count": 18,
          "exon_rank": 17,
          "exon_rank_end": null,
          "feature": "ENST00000674817.1",
          "gene_hgnc_id": 16877,
          "gene_symbol": "MFN2",
          "hgvs_c": "c.2119C>T",
          "hgvs_p": "p.Arg707Trp",
          "intron_rank": null,
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          "mane_plus": null,
          "mane_select": null,
          "protein_coding": true,
          "protein_id": "ENSP00000502151.1",
          "strand": true,
          "transcript": "ENST00000674817.1",
          "transcript_support_level": null
        },
        {
          "aa_alt": "W",
          "aa_end": null,
          "aa_length": 757,
          "aa_ref": "R",
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          "biotype": "protein_coding",
          "canonical": false,
          "cdna_end": null,
          "cdna_length": 4539,
          "cdna_start": 2449,
          "cds_end": null,
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          "consequences": [
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          ],
          "exon_count": 19,
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          "exon_rank_end": null,
          "feature": "ENST00000674910.1",
          "gene_hgnc_id": 16877,
          "gene_symbol": "MFN2",
          "hgvs_c": "c.2119C>T",
          "hgvs_p": "p.Arg707Trp",
          "intron_rank": null,
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          "mane_plus": null,
          "mane_select": null,
          "protein_coding": true,
          "protein_id": "ENSP00000501716.1",
          "strand": true,
          "transcript": "ENST00000674910.1",
          "transcript_support_level": null
        },
        {
          "aa_alt": "W",
          "aa_end": null,
          "aa_length": 757,
          "aa_ref": "R",
          "aa_start": 707,
          "biotype": "protein_coding",
          "canonical": false,
          "cdna_end": null,
          "cdna_length": 4555,
          "cdna_start": 2465,
          "cds_end": null,
          "cds_length": 2274,
          "cds_start": 2119,
          "consequences": [
            "missense_variant"
          ],
          "exon_count": 19,
          "exon_rank": 18,
          "exon_rank_end": null,
          "feature": "ENST00000675053.1",
          "gene_hgnc_id": 16877,
          "gene_symbol": "MFN2",
          "hgvs_c": "c.2119C>T",
          "hgvs_p": "p.Arg707Trp",
          "intron_rank": null,
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          "mane_plus": null,
          "mane_select": null,
          "protein_coding": true,
          "protein_id": "ENSP00000501646.1",
          "strand": true,
          "transcript": "ENST00000675053.1",
          "transcript_support_level": null
        },
        {
          "aa_alt": "W",
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          "aa_length": 757,
          "aa_ref": "R",
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          "biotype": "protein_coding",
          "canonical": false,
          "cdna_end": null,
          "cdna_length": 4461,
          "cdna_start": 2371,
          "cds_end": null,
          "cds_length": 2274,
          "cds_start": 2119,
          "consequences": [
            "missense_variant"
          ],
          "exon_count": 20,
          "exon_rank": 19,
          "exon_rank_end": null,
          "feature": "ENST00000675113.1",
          "gene_hgnc_id": 16877,
          "gene_symbol": "MFN2",
          "hgvs_c": "c.2119C>T",
          "hgvs_p": "p.Arg707Trp",
          "intron_rank": null,
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          "mane_plus": null,
          "mane_select": null,
          "protein_coding": true,
          "protein_id": "ENSP00000502623.1",
          "strand": true,
          "transcript": "ENST00000675113.1",
          "transcript_support_level": null
        },
        {
          "aa_alt": "W",
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          "aa_ref": "R",
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          "biotype": "protein_coding",
          "canonical": false,
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          "cdna_length": 4772,
          "cdna_start": 2682,
          "cds_end": null,
          "cds_length": 2274,
          "cds_start": 2119,
          "consequences": [
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          ],
          "exon_count": 20,
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          "exon_rank_end": null,
          "feature": "ENST00000675231.1",
          "gene_hgnc_id": 16877,
          "gene_symbol": "MFN2",
          "hgvs_c": "c.2119C>T",
          "hgvs_p": "p.Arg707Trp",
          "intron_rank": null,
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          "mane_plus": null,
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          "protein_coding": true,
          "protein_id": "ENSP00000502404.1",
          "strand": true,
          "transcript": "ENST00000675231.1",
          "transcript_support_level": null
        },
        {
          "aa_alt": "W",
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          "aa_length": 757,
          "aa_ref": "R",
          "aa_start": 707,
          "biotype": "protein_coding",
          "canonical": false,
          "cdna_end": null,
          "cdna_length": 4497,
          "cdna_start": 2399,
          "cds_end": null,
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          "cds_start": 2119,
          "consequences": [
            "missense_variant"
          ],
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          "exon_rank": 19,
          "exon_rank_end": null,
          "feature": "ENST00000675919.1",
          "gene_hgnc_id": 16877,
          "gene_symbol": "MFN2",
          "hgvs_c": "c.2119C>T",
          "hgvs_p": "p.Arg707Trp",
          "intron_rank": null,
          "intron_rank_end": null,
          "mane_plus": null,
          "mane_select": null,
          "protein_coding": true,
          "protein_id": "ENSP00000501776.1",
          "strand": true,
          "transcript": "ENST00000675919.1",
          "transcript_support_level": null
        },
        {
          "aa_alt": "W",
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          "aa_length": 757,
          "aa_ref": "R",
          "aa_start": 707,
          "biotype": "protein_coding",
          "canonical": false,
          "cdna_end": null,
          "cdna_length": 4529,
          "cdna_start": 2431,
          "cds_end": null,
          "cds_length": 2274,
          "cds_start": 2119,
          "consequences": [
            "missense_variant"
          ],
          "exon_count": 20,
          "exon_rank": 19,
          "exon_rank_end": null,
          "feature": "ENST00000676293.1",
          "gene_hgnc_id": 16877,
          "gene_symbol": "MFN2",
          "hgvs_c": "c.2119C>T",
          "hgvs_p": "p.Arg707Trp",
          "intron_rank": null,
          "intron_rank_end": null,
          "mane_plus": null,
          "mane_select": null,
          "protein_coding": true,
          "protein_id": "ENSP00000502362.1",
          "strand": true,
          "transcript": "ENST00000676293.1",
          "transcript_support_level": null
        },
        {
          "aa_alt": "W",
          "aa_end": null,
          "aa_length": 757,
          "aa_ref": "R",
          "aa_start": 707,
          "biotype": "protein_coding",
          "canonical": false,
          "cdna_end": null,
          "cdna_length": 4609,
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      "pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
      "phenotype_combined": "Charcot-Marie-Tooth disease, axonal, autosomal recessive, type 2a2b;|not provided|Charcot-Marie-Tooth disease type 2A2|Charcot-Marie-Tooth disease type 2|Inborn genetic diseases|MFN2-related disorder|Charcot-Marie-Tooth disease|Charcot-Marie-Tooth disease, axonal, autosomal recessive, type 2a2b;;Charcot-Marie-Tooth disease type 2A2|Peripheral axonal neuropathy|Charcot-Marie-Tooth disease, type 2A;Hereditary motor and sensory neuropathy with optic atrophy|Multiple symmetric lipomatosis|Neuropathy, hereditary motor and sensory, type 6A;Charcot-Marie-Tooth disease, axonal, autosomal recessive, type 2a2b;;Charcot-Marie-Tooth disease type 2A2|Neuropathy, hereditary motor and sensory, type 6A|Tip-toe gait",
      "phylop100way_prediction": "Benign",
      "phylop100way_score": 2.887,
      "pos": 12009641,
      "ref": "C",
      "revel_prediction": "Pathogenic",
      "revel_score": 0.839,
      "splice_prediction_selected": "Benign",
      "splice_score_selected": 0,
      "splice_source_selected": "max_spliceai",
      "spliceai_max_prediction": "Benign",
      "spliceai_max_score": 0,
      "transcript": "NM_014874.4"
    }
  ]
}
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