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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: 1-156809289-C-G (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=156809289&ref=C&alt=G&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "1",
      "pos": 156809289,
      "ref": "C",
      "alt": "G",
      "effect": "missense_variant",
      "transcript": "ENST00000368199.8",
      "consequences": [
        {
          "aa_ref": "V",
          "aa_alt": "L",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 7,
          "exon_rank_end": null,
          "exon_count": 9,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SH2D2A",
          "gene_hgnc_id": 10821,
          "hgvs_c": "c.916G>C",
          "hgvs_p": "p.Val306Leu",
          "transcript": "NM_003975.4",
          "protein_id": "NP_003966.2",
          "transcript_support_level": null,
          "aa_start": 306,
          "aa_end": null,
          "aa_length": 389,
          "cds_start": 916,
          "cds_end": null,
          "cds_length": 1170,
          "cdna_start": 1056,
          "cdna_end": null,
          "cdna_length": 1644,
          "mane_select": "ENST00000368199.8",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "V",
          "aa_alt": "L",
          "canonical": true,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 7,
          "exon_rank_end": null,
          "exon_count": 9,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SH2D2A",
          "gene_hgnc_id": 10821,
          "hgvs_c": "c.916G>C",
          "hgvs_p": "p.Val306Leu",
          "transcript": "ENST00000368199.8",
          "protein_id": "ENSP00000357182.3",
          "transcript_support_level": 1,
          "aa_start": 306,
          "aa_end": null,
          "aa_length": 389,
          "cds_start": 916,
          "cds_end": null,
          "cds_length": 1170,
          "cdna_start": 1056,
          "cdna_end": null,
          "cdna_length": 1644,
          "mane_select": "NM_003975.4",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "V",
          "aa_alt": "L",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 7,
          "exon_rank_end": null,
          "exon_count": 9,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SH2D2A",
          "gene_hgnc_id": 10821,
          "hgvs_c": "c.946G>C",
          "hgvs_p": "p.Val316Leu",
          "transcript": "ENST00000392306.2",
          "protein_id": "ENSP00000376123.2",
          "transcript_support_level": 1,
          "aa_start": 316,
          "aa_end": null,
          "aa_length": 399,
          "cds_start": 946,
          "cds_end": null,
          "cds_length": 1200,
          "cdna_start": 1086,
          "cdna_end": null,
          "cdna_length": 1673,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "V",
          "aa_alt": "L",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 7,
          "exon_rank_end": null,
          "exon_count": 9,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SH2D2A",
          "gene_hgnc_id": 10821,
          "hgvs_c": "c.862G>C",
          "hgvs_p": "p.Val288Leu",
          "transcript": "ENST00000368198.8",
          "protein_id": "ENSP00000357181.3",
          "transcript_support_level": 1,
          "aa_start": 288,
          "aa_end": null,
          "aa_length": 371,
          "cds_start": 862,
          "cds_end": null,
          "cds_length": 1116,
          "cdna_start": 1011,
          "cdna_end": null,
          "cdna_length": 1602,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "V",
          "aa_alt": "L",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 7,
          "exon_rank_end": null,
          "exon_count": 9,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SH2D2A",
          "gene_hgnc_id": 10821,
          "hgvs_c": "c.946G>C",
          "hgvs_p": "p.Val316Leu",
          "transcript": "NM_001161441.2",
          "protein_id": "NP_001154913.1",
          "transcript_support_level": null,
          "aa_start": 316,
          "aa_end": null,
          "aa_length": 399,
          "cds_start": 946,
          "cds_end": null,
          "cds_length": 1200,
          "cdna_start": 1086,
          "cdna_end": null,
          "cdna_length": 1674,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "V",
          "aa_alt": "L",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 7,
          "exon_rank_end": null,
          "exon_count": 8,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SH2D2A",
          "gene_hgnc_id": 10821,
          "hgvs_c": "c.916G>C",
          "hgvs_p": "p.Val306Leu",
          "transcript": "NM_001161444.2",
          "protein_id": "NP_001154916.1",
          "transcript_support_level": null,
          "aa_start": 306,
          "aa_end": null,
          "aa_length": 389,
          "cds_start": 916,
          "cds_end": null,
          "cds_length": 1170,
          "cdna_start": 1056,
          "cdna_end": null,
          "cdna_length": 1431,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "V",
          "aa_alt": "L",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 7,
          "exon_rank_end": null,
          "exon_count": 9,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SH2D2A",
          "gene_hgnc_id": 10821,
          "hgvs_c": "c.862G>C",
          "hgvs_p": "p.Val288Leu",
          "transcript": "NM_001161442.2",
          "protein_id": "NP_001154914.1",
          "transcript_support_level": null,
          "aa_start": 288,
          "aa_end": null,
          "aa_length": 371,
          "cds_start": 862,
          "cds_end": null,
          "cds_length": 1116,
          "cdna_start": 1025,
          "cdna_end": null,
          "cdna_length": 1613,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "V",
          "aa_alt": "L",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 6,
          "exon_rank_end": null,
          "exon_count": 8,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SH2D2A",
          "gene_hgnc_id": 10821,
          "hgvs_c": "c.832G>C",
          "hgvs_p": "p.Val278Leu",
          "transcript": "NM_001161443.2",
          "protein_id": "NP_001154915.1",
          "transcript_support_level": null,
          "aa_start": 278,
          "aa_end": null,
          "aa_length": 361,
          "cds_start": 832,
          "cds_end": null,
          "cds_length": 1086,
          "cdna_start": 1245,
          "cdna_end": null,
          "cdna_length": 1833,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "V",
          "aa_alt": "L",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 7,
          "exon_rank_end": null,
          "exon_count": 9,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SH2D2A",
          "gene_hgnc_id": 10821,
          "hgvs_c": "c.964G>C",
          "hgvs_p": "p.Val322Leu",
          "transcript": "XM_017002762.3",
          "protein_id": "XP_016858251.1",
          "transcript_support_level": null,
          "aa_start": 322,
          "aa_end": null,
          "aa_length": 405,
          "cds_start": 964,
          "cds_end": null,
          "cds_length": 1218,
          "cdna_start": 1104,
          "cdna_end": null,
          "cdna_length": 1692,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "V",
          "aa_alt": "L",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 7,
          "exon_rank_end": null,
          "exon_count": 9,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SH2D2A",
          "gene_hgnc_id": 10821,
          "hgvs_c": "c.934G>C",
          "hgvs_p": "p.Val312Leu",
          "transcript": "XM_006711615.3",
          "protein_id": "XP_006711678.1",
          "transcript_support_level": null,
          "aa_start": 312,
          "aa_end": null,
          "aa_length": 395,
          "cds_start": 934,
          "cds_end": null,
          "cds_length": 1188,
          "cdna_start": 1074,
          "cdna_end": null,
          "cdna_length": 1662,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "V",
          "aa_alt": "L",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 7,
          "exon_rank_end": null,
          "exon_count": 9,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SH2D2A",
          "gene_hgnc_id": 10821,
          "hgvs_c": "c.904G>C",
          "hgvs_p": "p.Val302Leu",
          "transcript": "XM_017002764.3",
          "protein_id": "XP_016858253.1",
          "transcript_support_level": null,
          "aa_start": 302,
          "aa_end": null,
          "aa_length": 385,
          "cds_start": 904,
          "cds_end": null,
          "cds_length": 1158,
          "cdna_start": 1044,
          "cdna_end": null,
          "cdna_length": 1632,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "V",
          "aa_alt": "L",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 7,
          "exon_rank_end": null,
          "exon_count": 9,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SH2D2A",
          "gene_hgnc_id": 10821,
          "hgvs_c": "c.892G>C",
          "hgvs_p": "p.Val298Leu",
          "transcript": "XM_017002765.2",
          "protein_id": "XP_016858254.1",
          "transcript_support_level": null,
          "aa_start": 298,
          "aa_end": null,
          "aa_length": 381,
          "cds_start": 892,
          "cds_end": null,
          "cds_length": 1146,
          "cdna_start": 1055,
          "cdna_end": null,
          "cdna_length": 1643,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "V",
          "aa_alt": "L",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 7,
          "exon_rank_end": null,
          "exon_count": 9,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SH2D2A",
          "gene_hgnc_id": 10821,
          "hgvs_c": "c.880G>C",
          "hgvs_p": "p.Val294Leu",
          "transcript": "XM_017002766.2",
          "protein_id": "XP_016858255.1",
          "transcript_support_level": null,
          "aa_start": 294,
          "aa_end": null,
          "aa_length": 377,
          "cds_start": 880,
          "cds_end": null,
          "cds_length": 1134,
          "cdna_start": 1043,
          "cdna_end": null,
          "cdna_length": 1631,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "V",
          "aa_alt": "L",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 7,
          "exon_rank_end": null,
          "exon_count": 7,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SH2D2A",
          "gene_hgnc_id": 10821,
          "hgvs_c": "c.964G>C",
          "hgvs_p": "p.Val322Leu",
          "transcript": "XM_047433652.1",
          "protein_id": "XP_047289608.1",
          "transcript_support_level": null,
          "aa_start": 322,
          "aa_end": null,
          "aa_length": 371,
          "cds_start": 964,
          "cds_end": null,
          "cds_length": 1116,
          "cdna_start": 1104,
          "cdna_end": null,
          "cdna_length": 4150,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "V",
          "aa_alt": "L",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 7,
          "exon_rank_end": null,
          "exon_count": 9,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SH2D2A",
          "gene_hgnc_id": 10821,
          "hgvs_c": "c.850G>C",
          "hgvs_p": "p.Val284Leu",
          "transcript": "XM_047433655.1",
          "protein_id": "XP_047289611.1",
          "transcript_support_level": null,
          "aa_start": 284,
          "aa_end": null,
          "aa_length": 367,
          "cds_start": 850,
          "cds_end": null,
          "cds_length": 1104,
          "cdna_start": 1013,
          "cdna_end": null,
          "cdna_length": 1601,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": false,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 3,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SH2D2A",
          "gene_hgnc_id": 10821,
          "hgvs_c": "n.613G>C",
          "hgvs_p": null,
          "transcript": "ENST00000468744.5",
          "protein_id": null,
          "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": 699,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        }
      ],
      "gene_symbol": "SH2D2A",
      "gene_hgnc_id": 10821,
      "dbsnp": "rs142571523",
      "frequency_reference_population": 0.000045227785,
      "hom_count_reference_population": 0,
      "allele_count_reference_population": 73,
      "gnomad_exomes_af": 0.0000458323,
      "gnomad_genomes_af": 0.0000394213,
      "gnomad_exomes_ac": 67,
      "gnomad_genomes_ac": 6,
      "gnomad_exomes_homalt": 0,
      "gnomad_genomes_homalt": 0,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": 0.07282167673110962,
      "computational_prediction_selected": "Benign",
      "computational_source_selected": "MetaRNN",
      "splice_score_selected": 0,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": 0.038,
      "revel_prediction": "Benign",
      "alphamissense_score": 0.2555,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": -0.6,
      "bayesdelnoaf_prediction": "Benign",
      "phylop100way_score": 0.693,
      "phylop100way_prediction": "Benign",
      "spliceai_max_score": 0,
      "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": 0,
      "acmg_classification": "Uncertain_significance",
      "acmg_criteria": "PM2,BP4_Moderate",
      "acmg_by_gene": [
        {
          "score": 0,
          "benign_score": 2,
          "pathogenic_score": 2,
          "criteria": [
            "PM2",
            "BP4_Moderate"
          ],
          "verdict": "Uncertain_significance",
          "transcript": "ENST00000368199.8",
          "gene_symbol": "SH2D2A",
          "hgnc_id": 10821,
          "effects": [
            "missense_variant"
          ],
          "inheritance_mode": "",
          "hgvs_c": "c.916G>C",
          "hgvs_p": "p.Val306Leu"
        }
      ],
      "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
}