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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: 1-40301350-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=40301350&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 6,
"criteria": [
"BP4_Strong",
"BP6",
"BP7"
],
"effects": [
"synonymous_variant"
],
"gene_symbol": "COL9A2",
"hgnc_id": 2218,
"hgvs_c": "c.1902C>T",
"hgvs_p": "p.Asn634Asn",
"inheritance_mode": "AR,AD",
"pathogenic_score": 0,
"score": -6,
"transcript": "NM_001852.4",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Strong,BP6,BP7",
"acmg_score": -6,
"allele_count_reference_population": 121,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.72,
"chr": "1",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_disease": " 2, multiple,Epiphyseal dysplasia,not provided,not specified",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:3",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.7200000286102295,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 689,
"aa_ref": "N",
"aa_start": 634,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2852,
"cdna_start": 1991,
"cds_end": null,
"cds_length": 2070,
"cds_start": 1902,
"consequences": [
"synonymous_variant"
],
"exon_count": 32,
"exon_rank": 32,
"exon_rank_end": null,
"feature": "NM_001852.4",
"gene_hgnc_id": 2218,
"gene_symbol": "COL9A2",
"hgvs_c": "c.1902C>T",
"hgvs_p": "p.Asn634Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000372748.8",
"protein_coding": true,
"protein_id": "NP_001843.1",
"strand": false,
"transcript": "NM_001852.4",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 689,
"aa_ref": "N",
"aa_start": 634,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2852,
"cdna_start": 1991,
"cds_end": null,
"cds_length": 2070,
"cds_start": 1902,
"consequences": [
"synonymous_variant"
],
"exon_count": 32,
"exon_rank": 32,
"exon_rank_end": null,
"feature": "ENST00000372748.8",
"gene_hgnc_id": 2218,
"gene_symbol": "COL9A2",
"hgvs_c": "c.1902C>T",
"hgvs_p": "p.Asn634Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001852.4",
"protein_coding": true,
"protein_id": "ENSP00000361834.3",
"strand": false,
"transcript": "ENST00000372748.8",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 2887,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 31,
"exon_rank": 31,
"exon_rank_end": null,
"feature": "ENST00000482722.5",
"gene_hgnc_id": 2218,
"gene_symbol": "COL9A2",
"hgvs_c": "n.2205C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000482722.5",
"transcript_support_level": 1
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 717,
"aa_ref": "N",
"aa_start": 662,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2892,
"cdna_start": 2071,
"cds_end": null,
"cds_length": 2154,
"cds_start": 1986,
"consequences": [
"synonymous_variant"
],
"exon_count": 32,
"exon_rank": 32,
"exon_rank_end": null,
"feature": "ENST00000869268.1",
"gene_hgnc_id": 2218,
"gene_symbol": "COL9A2",
"hgvs_c": "c.1986C>T",
"hgvs_p": "p.Asn662Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000539327.1",
"strand": false,
"transcript": "ENST00000869268.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 693,
"aa_ref": "N",
"aa_start": 638,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2926,
"cdna_start": 2063,
"cds_end": null,
"cds_length": 2082,
"cds_start": 1914,
"consequences": [
"synonymous_variant"
],
"exon_count": 33,
"exon_rank": 33,
"exon_rank_end": null,
"feature": "ENST00000869264.1",
"gene_hgnc_id": 2218,
"gene_symbol": "COL9A2",
"hgvs_c": "c.1914C>T",
"hgvs_p": "p.Asn638Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000539323.1",
"strand": false,
"transcript": "ENST00000869264.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 682,
"aa_ref": "N",
"aa_start": 627,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2814,
"cdna_start": 1993,
"cds_end": null,
"cds_length": 2049,
"cds_start": 1881,
"consequences": [
"synonymous_variant"
],
"exon_count": 32,
"exon_rank": 32,
"exon_rank_end": null,
"feature": "ENST00000869265.1",
"gene_hgnc_id": 2218,
"gene_symbol": "COL9A2",
"hgvs_c": "c.1881C>T",
"hgvs_p": "p.Asn627Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000539324.1",
"strand": false,
"transcript": "ENST00000869265.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 671,
"aa_ref": "N",
"aa_start": 616,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2763,
"cdna_start": 1936,
"cds_end": null,
"cds_length": 2016,
"cds_start": 1848,
"consequences": [
"synonymous_variant"
],
"exon_count": 31,
"exon_rank": 31,
"exon_rank_end": null,
"feature": "ENST00000869266.1",
"gene_hgnc_id": 2218,
"gene_symbol": "COL9A2",
"hgvs_c": "c.1848C>T",
"hgvs_p": "p.Asn616Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000539325.1",
"strand": false,
"transcript": "ENST00000869266.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 638,
"aa_ref": "N",
"aa_start": 583,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2661,
"cdna_start": 1834,
"cds_end": null,
"cds_length": 1917,
"cds_start": 1749,
"consequences": [
"synonymous_variant"
],
"exon_count": 29,
"exon_rank": 29,
"exon_rank_end": null,
"feature": "ENST00000869267.1",
"gene_hgnc_id": 2218,
"gene_symbol": "COL9A2",
"hgvs_c": "c.1749C>T",
"hgvs_p": "p.Asn583Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000539326.1",
"strand": false,
"transcript": "ENST00000869267.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 693,
"aa_ref": "N",
"aa_start": 638,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2864,
"cdna_start": 2003,
"cds_end": null,
"cds_length": 2082,
"cds_start": 1914,
"consequences": [
"synonymous_variant"
],
"exon_count": 32,
"exon_rank": 32,
"exon_rank_end": null,
"feature": "XM_017000332.2",
"gene_hgnc_id": 2218,
"gene_symbol": "COL9A2",
"hgvs_c": "c.1914C>T",
"hgvs_p": "p.Asn638Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016855821.1",
"strand": false,
"transcript": "XM_017000332.2",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 599,
"aa_ref": "N",
"aa_start": 544,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2958,
"cdna_start": 2097,
"cds_end": null,
"cds_length": 1800,
"cds_start": 1632,
"consequences": [
"synonymous_variant"
],
"exon_count": 32,
"exon_rank": 32,
"exon_rank_end": null,
"feature": "XM_011540715.3",
"gene_hgnc_id": 2218,
"gene_symbol": "COL9A2",
"hgvs_c": "c.1632C>T",
"hgvs_p": "p.Asn544Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011539017.1",
"strand": false,
"transcript": "XM_011540715.3",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 599,
"aa_ref": "N",
"aa_start": 544,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2804,
"cdna_start": 1943,
"cds_end": null,
"cds_length": 1800,
"cds_start": 1632,
"consequences": [
"synonymous_variant"
],
"exon_count": 31,
"exon_rank": 31,
"exon_rank_end": null,
"feature": "XM_011540716.3",
"gene_hgnc_id": 2218,
"gene_symbol": "COL9A2",
"hgvs_c": "c.1632C>T",
"hgvs_p": "p.Asn544Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011539018.1",
"strand": false,
"transcript": "XM_011540716.3",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 595,
"aa_ref": "N",
"aa_start": 540,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2792,
"cdna_start": 1931,
"cds_end": null,
"cds_length": 1788,
"cds_start": 1620,
"consequences": [
"synonymous_variant"
],
"exon_count": 31,
"exon_rank": 31,
"exon_rank_end": null,
"feature": "XM_017000333.2",
"gene_hgnc_id": 2218,
"gene_symbol": "COL9A2",
"hgvs_c": "c.1620C>T",
"hgvs_p": "p.Asn540Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016855822.1",
"strand": false,
"transcript": "XM_017000333.2",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs781428852",
"effect": "synonymous_variant",
"frequency_reference_population": 0.000075197786,
"gene_hgnc_id": 2218,
"gene_symbol": "COL9A2",
"gnomad_exomes_ac": 113,
"gnomad_exomes_af": 0.0000775709,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 8,
"gnomad_genomes_af": 0.0000525079,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"phenotype_combined": "not specified|Epiphyseal dysplasia, multiple, 2|not provided",
"phylop100way_prediction": "Benign",
"phylop100way_score": -0.461,
"pos": 40301350,
"ref": "G",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_001852.4"
}
]
}