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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: 2-230996495-G-A (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=230996495&ref=G&alt=A&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "2",
      "pos": 230996495,
      "ref": "G",
      "alt": "A",
      "effect": "missense_variant",
      "transcript": "NM_139073.5",
      "consequences": [
        {
          "aa_ref": "D",
          "aa_alt": "N",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 5,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SPATA3",
          "gene_hgnc_id": 17884,
          "hgvs_c": "c.262G>A",
          "hgvs_p": "p.Asp88Asn",
          "transcript": "NM_139073.5",
          "protein_id": "NP_620712.2",
          "transcript_support_level": null,
          "aa_start": 88,
          "aa_end": null,
          "aa_length": 192,
          "cds_start": 262,
          "cds_end": null,
          "cds_length": 579,
          "cdna_start": 375,
          "cdna_end": null,
          "cdna_length": 1629,
          "mane_select": "ENST00000433428.7",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "D",
          "aa_alt": "N",
          "canonical": true,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 5,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SPATA3",
          "gene_hgnc_id": 17884,
          "hgvs_c": "c.262G>A",
          "hgvs_p": "p.Asp88Asn",
          "transcript": "ENST00000433428.7",
          "protein_id": "ENSP00000403804.2",
          "transcript_support_level": 1,
          "aa_start": 88,
          "aa_end": null,
          "aa_length": 192,
          "cds_start": 262,
          "cds_end": null,
          "cds_length": 579,
          "cdna_start": 375,
          "cdna_end": null,
          "cdna_length": 1629,
          "mane_select": "NM_139073.5",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "D",
          "aa_alt": "N",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 6,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SPATA3",
          "gene_hgnc_id": 17884,
          "hgvs_c": "c.262G>A",
          "hgvs_p": "p.Asp88Asn",
          "transcript": "ENST00000424440.5",
          "protein_id": "ENSP00000399514.1",
          "transcript_support_level": 1,
          "aa_start": 88,
          "aa_end": null,
          "aa_length": 192,
          "cds_start": 262,
          "cds_end": null,
          "cds_length": 579,
          "cdna_start": 375,
          "cdna_end": null,
          "cdna_length": 1011,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "D",
          "aa_alt": "N",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 9,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SPATA3",
          "gene_hgnc_id": 17884,
          "hgvs_c": "c.262G>A",
          "hgvs_p": "p.Asp88Asn",
          "transcript": "ENST00000452881.5",
          "protein_id": "ENSP00000388895.1",
          "transcript_support_level": 2,
          "aa_start": 88,
          "aa_end": null,
          "aa_length": 192,
          "cds_start": 262,
          "cds_end": null,
          "cds_length": 579,
          "cdna_start": 370,
          "cdna_end": null,
          "cdna_length": 1618,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "D",
          "aa_alt": "N",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 5,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SPATA3",
          "gene_hgnc_id": 17884,
          "hgvs_c": "c.262G>A",
          "hgvs_p": "p.Asp88Asn",
          "transcript": "ENST00000455816.1",
          "protein_id": "ENSP00000388741.1",
          "transcript_support_level": 5,
          "aa_start": 88,
          "aa_end": null,
          "aa_length": 192,
          "cds_start": 262,
          "cds_end": null,
          "cds_length": 579,
          "cdna_start": 262,
          "cdna_end": null,
          "cdna_length": 766,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "D",
          "aa_alt": "N",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 3,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SPATA3",
          "gene_hgnc_id": 17884,
          "hgvs_c": "c.160G>A",
          "hgvs_p": "p.Asp54Asn",
          "transcript": "ENST00000440792.5",
          "protein_id": "ENSP00000404510.1",
          "transcript_support_level": 5,
          "aa_start": 54,
          "aa_end": null,
          "aa_length": 104,
          "cds_start": 160,
          "cds_end": null,
          "cds_length": 315,
          "cdna_start": 160,
          "cdna_end": null,
          "cdna_length": 406,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "D",
          "aa_alt": "N",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 4,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SPATA3",
          "gene_hgnc_id": 17884,
          "hgvs_c": "c.106G>A",
          "hgvs_p": "p.Asp36Asn",
          "transcript": "ENST00000423134.1",
          "protein_id": "ENSP00000411374.1",
          "transcript_support_level": 2,
          "aa_start": 36,
          "aa_end": null,
          "aa_length": 86,
          "cds_start": 106,
          "cds_end": null,
          "cds_length": 261,
          "cdna_start": 107,
          "cdna_end": null,
          "cdna_length": 433,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "D",
          "aa_alt": "N",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 4,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SPATA3",
          "gene_hgnc_id": 17884,
          "hgvs_c": "c.262G>A",
          "hgvs_p": "p.Asp88Asn",
          "transcript": "XM_047443397.1",
          "protein_id": "XP_047299353.1",
          "transcript_support_level": null,
          "aa_start": 88,
          "aa_end": null,
          "aa_length": 213,
          "cds_start": 262,
          "cds_end": null,
          "cds_length": 642,
          "cdna_start": 375,
          "cdna_end": null,
          "cdna_length": 1602,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "D",
          "aa_alt": "N",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 4,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SPATA3",
          "gene_hgnc_id": 17884,
          "hgvs_c": "c.262G>A",
          "hgvs_p": "p.Asp88Asn",
          "transcript": "XM_047443398.1",
          "protein_id": "XP_047299354.1",
          "transcript_support_level": null,
          "aa_start": 88,
          "aa_end": null,
          "aa_length": 213,
          "cds_start": 262,
          "cds_end": null,
          "cds_length": 642,
          "cdna_start": 375,
          "cdna_end": null,
          "cdna_length": 1002,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "D",
          "aa_alt": "N",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 4,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SPATA3",
          "gene_hgnc_id": 17884,
          "hgvs_c": "c.262G>A",
          "hgvs_p": "p.Asp88Asn",
          "transcript": "XM_005246303.3",
          "protein_id": "XP_005246360.1",
          "transcript_support_level": null,
          "aa_start": 88,
          "aa_end": null,
          "aa_length": 192,
          "cds_start": 262,
          "cds_end": null,
          "cds_length": 579,
          "cdna_start": 375,
          "cdna_end": null,
          "cdna_length": 1549,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "D",
          "aa_alt": "N",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 4,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SPATA3",
          "gene_hgnc_id": 17884,
          "hgvs_c": "c.262G>A",
          "hgvs_p": "p.Asp88Asn",
          "transcript": "XM_017003363.3",
          "protein_id": "XP_016858852.1",
          "transcript_support_level": null,
          "aa_start": 88,
          "aa_end": null,
          "aa_length": 192,
          "cds_start": 262,
          "cds_end": null,
          "cds_length": 579,
          "cdna_start": 375,
          "cdna_end": null,
          "cdna_length": 944,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 5,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SPATA3",
          "gene_hgnc_id": 17884,
          "hgvs_c": "n.375G>A",
          "hgvs_p": null,
          "transcript": "XR_001738624.3",
          "protein_id": null,
          "transcript_support_level": null,
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          "aa_length": null,
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          "cdna_start": null,
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          "cdna_length": 1024,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 6,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SPATA3",
          "gene_hgnc_id": 17884,
          "hgvs_c": "n.375G>A",
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          "transcript": "XR_001738627.3",
          "protein_id": null,
          "transcript_support_level": null,
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          "cdna_length": 1497,
          "mane_select": null,
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          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
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          "protein_coding": false,
          "strand": true,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 6,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SPATA3",
          "gene_hgnc_id": 17884,
          "hgvs_c": "n.375G>A",
          "hgvs_p": null,
          "transcript": "XR_001738628.2",
          "protein_id": null,
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": -4,
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          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 1319,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 5,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SPATA3",
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          "hgvs_c": "n.375G>A",
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          "mane_select": null,
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          "biotype": null,
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        },
        {
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          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 5,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SPATA3",
          "gene_hgnc_id": 17884,
          "hgvs_c": "n.375G>A",
          "hgvs_p": null,
          "transcript": "XR_007069639.1",
          "protein_id": null,
          "transcript_support_level": null,
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          "cdna_length": 1682,
          "mane_select": null,
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          "biotype": null,
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        },
        {
          "aa_ref": null,
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          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 5,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SPATA3",
          "gene_hgnc_id": 17884,
          "hgvs_c": "n.375G>A",
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          "transcript": "XR_007069640.1",
          "protein_id": null,
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          "cdna_length": 1081,
          "mane_select": null,
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          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 5,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SPATA3",
          "gene_hgnc_id": 17884,
          "hgvs_c": "n.375G>A",
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        },
        {
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          "strand": true,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 1,
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          "exon_count": 5,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SPATA3",
          "gene_hgnc_id": 17884,
          "hgvs_c": "n.375G>A",
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        },
        {
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          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 6,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SPATA3",
          "gene_hgnc_id": 17884,
          "hgvs_c": "n.375G>A",
          "hgvs_p": null,
          "transcript": "XR_922856.3",
          "protein_id": null,
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          "cds_length": null,
          "cdna_start": null,
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          "cdna_length": 1791,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 3,
          "intron_rank": 1,
          "intron_rank_end": null,
          "gene_symbol": "SPATA3",
          "gene_hgnc_id": 17884,
          "hgvs_c": "c.791-3871G>A",
          "hgvs_p": null,
          "transcript": "ENST00000645363.1",
          "protein_id": "ENSP00000494655.1",
          "transcript_support_level": null,
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          "aa_length": 355,
          "cds_start": -4,
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          "cds_length": 1068,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 1068,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "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": 3,
          "intron_rank": 1,
          "intron_rank_end": null,
          "gene_symbol": "SPATA3",
          "gene_hgnc_id": 17884,
          "hgvs_c": "n.23+239G>A",
          "hgvs_p": null,
          "transcript": "ENST00000454918.1",
          "protein_id": "ENSP00000395644.1",
          "transcript_support_level": 2,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 332,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        }
      ],
      "gene_symbol": "SPATA3",
      "gene_hgnc_id": 17884,
      "dbsnp": "rs149976648",
      "frequency_reference_population": 0.0062628286,
      "hom_count_reference_population": 46,
      "allele_count_reference_population": 9721,
      "gnomad_exomes_af": 0.00647924,
      "gnomad_genomes_af": 0.00427395,
      "gnomad_exomes_ac": 9070,
      "gnomad_genomes_ac": 651,
      "gnomad_exomes_homalt": 43,
      "gnomad_genomes_homalt": 3,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": 0.004458606243133545,
      "computational_prediction_selected": "Benign",
      "computational_source_selected": "MetaRNN",
      "splice_score_selected": 0.009999999776482582,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": 0.013,
      "revel_prediction": "Benign",
      "alphamissense_score": 0.1038,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": -0.72,
      "bayesdelnoaf_prediction": "Benign",
      "phylop100way_score": -0.397,
      "phylop100way_prediction": "Benign",
      "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": -10,
      "acmg_classification": "Benign",
      "acmg_criteria": "BP4_Strong,BP6_Moderate,BS2",
      "acmg_by_gene": [
        {
          "score": -10,
          "benign_score": 10,
          "pathogenic_score": 0,
          "criteria": [
            "BP4_Strong",
            "BP6_Moderate",
            "BS2"
          ],
          "verdict": "Benign",
          "transcript": "NM_139073.5",
          "gene_symbol": "SPATA3",
          "hgnc_id": 17884,
          "effects": [
            "missense_variant"
          ],
          "inheritance_mode": "AR",
          "hgvs_c": "c.262G>A",
          "hgvs_p": "p.Asp88Asn"
        }
      ],
      "clinvar_disease": "not provided",
      "clinvar_classification": "Likely benign",
      "clinvar_review_status": "criteria provided, single submitter",
      "clinvar_submissions_summary": "LB:1",
      "phenotype_combined": "not provided",
      "pathogenicity_classification_combined": "Likely benign",
      "custom_annotations": null
    }
  ],
  "message": null
}