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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: 12-47978329-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=47978329&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 47978329,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_001844.5",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 43,
"exon_rank_end": null,
"exon_count": 54,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL2A1",
"gene_hgnc_id": 2200,
"hgvs_c": "c.2965C>T",
"hgvs_p": "p.Arg989Cys",
"transcript": "NM_001844.5",
"protein_id": "NP_001835.3",
"transcript_support_level": null,
"aa_start": 989,
"aa_end": null,
"aa_length": 1487,
"cds_start": 2965,
"cds_end": null,
"cds_length": 4464,
"cdna_start": 3120,
"cdna_end": null,
"cdna_length": 5059,
"mane_select": "ENST00000380518.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 43,
"exon_rank_end": null,
"exon_count": 54,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL2A1",
"gene_hgnc_id": 2200,
"hgvs_c": "c.2965C>T",
"hgvs_p": "p.Arg989Cys",
"transcript": "ENST00000380518.8",
"protein_id": "ENSP00000369889.3",
"transcript_support_level": 1,
"aa_start": 989,
"aa_end": null,
"aa_length": 1487,
"cds_start": 2965,
"cds_end": null,
"cds_length": 4464,
"cdna_start": 3120,
"cdna_end": null,
"cdna_length": 5059,
"mane_select": "NM_001844.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 42,
"exon_rank_end": null,
"exon_count": 53,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL2A1",
"gene_hgnc_id": 2200,
"hgvs_c": "c.2758C>T",
"hgvs_p": "p.Arg920Cys",
"transcript": "ENST00000337299.7",
"protein_id": "ENSP00000338213.6",
"transcript_support_level": 1,
"aa_start": 920,
"aa_end": null,
"aa_length": 1418,
"cds_start": 2758,
"cds_end": null,
"cds_length": 4257,
"cdna_start": 2943,
"cdna_end": null,
"cdna_length": 4442,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 42,
"exon_rank_end": null,
"exon_count": 53,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL2A1",
"gene_hgnc_id": 2200,
"hgvs_c": "c.2758C>T",
"hgvs_p": "p.Arg920Cys",
"transcript": "NM_033150.3",
"protein_id": "NP_149162.2",
"transcript_support_level": null,
"aa_start": 920,
"aa_end": null,
"aa_length": 1418,
"cds_start": 2758,
"cds_end": null,
"cds_length": 4257,
"cdna_start": 2913,
"cdna_end": null,
"cdna_length": 4852,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 45,
"exon_rank_end": null,
"exon_count": 56,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL2A1",
"gene_hgnc_id": 2200,
"hgvs_c": "c.3109C>T",
"hgvs_p": "p.Arg1037Cys",
"transcript": "XM_017018828.1",
"protein_id": "XP_016874317.1",
"transcript_support_level": null,
"aa_start": 1037,
"aa_end": null,
"aa_length": 1535,
"cds_start": 3109,
"cds_end": null,
"cds_length": 4608,
"cdna_start": 3231,
"cdna_end": null,
"cdna_length": 5170,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 45,
"exon_rank_end": null,
"exon_count": 56,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL2A1",
"gene_hgnc_id": 2200,
"hgvs_c": "c.3106C>T",
"hgvs_p": "p.Arg1036Cys",
"transcript": "XM_017018829.1",
"protein_id": "XP_016874318.1",
"transcript_support_level": null,
"aa_start": 1036,
"aa_end": null,
"aa_length": 1534,
"cds_start": 3106,
"cds_end": null,
"cds_length": 4605,
"cdna_start": 3228,
"cdna_end": null,
"cdna_length": 5167,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 44,
"exon_rank_end": null,
"exon_count": 55,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL2A1",
"gene_hgnc_id": 2200,
"hgvs_c": "c.2899C>T",
"hgvs_p": "p.Arg967Cys",
"transcript": "XM_017018830.1",
"protein_id": "XP_016874319.1",
"transcript_support_level": null,
"aa_start": 967,
"aa_end": null,
"aa_length": 1465,
"cds_start": 2899,
"cds_end": null,
"cds_length": 4398,
"cdna_start": 3021,
"cdna_end": null,
"cdna_length": 4960,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 43,
"exon_rank_end": null,
"exon_count": 54,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL2A1",
"gene_hgnc_id": 2200,
"hgvs_c": "c.2419C>T",
"hgvs_p": "p.Arg807Cys",
"transcript": "XM_017018831.3",
"protein_id": "XP_016874320.1",
"transcript_support_level": null,
"aa_start": 807,
"aa_end": null,
"aa_length": 1305,
"cds_start": 2419,
"cds_end": null,
"cds_length": 3918,
"cdna_start": 3449,
"cdna_end": null,
"cdna_length": 5388,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 43,
"exon_rank_end": null,
"exon_count": 54,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL2A1",
"gene_hgnc_id": 2200,
"hgvs_c": "c.2419C>T",
"hgvs_p": "p.Arg807Cys",
"transcript": "XM_047428315.1",
"protein_id": "XP_047284271.1",
"transcript_support_level": null,
"aa_start": 807,
"aa_end": null,
"aa_length": 1305,
"cds_start": 2419,
"cds_end": null,
"cds_length": 3918,
"cdna_start": 2898,
"cdna_end": null,
"cdna_length": 4837,
"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": 26,
"exon_rank_end": null,
"exon_count": 37,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL2A1",
"gene_hgnc_id": 2200,
"hgvs_c": "n.2051C>T",
"hgvs_p": null,
"transcript": "ENST00000493991.5",
"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": 3756,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "COL2A1",
"gene_hgnc_id": 2200,
"dbsnp": "rs121912874",
"frequency_reference_population": 6.841246e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.84125e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.973945677280426,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.20000000298023224,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.947,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9714,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.46,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 5.757,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.2,
"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": 19,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM1,PM2,PM5,PP2,PP3_Strong,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 19,
"benign_score": 0,
"pathogenic_score": 19,
"criteria": [
"PM1",
"PM2",
"PM5",
"PP2",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "NM_001844.5",
"gene_symbol": "COL2A1",
"hgnc_id": 2200,
"effects": [
"missense_variant"
],
"inheritance_mode": "Unknown,AD,AR",
"hgvs_c": "c.2965C>T",
"hgvs_p": "p.Arg989Cys"
}
],
"clinvar_disease": " Stanescu type,14 conditions,Spondyloepiphyseal dysplasia,Spondyloepiphyseal dysplasia congenita,Spondyloperipheral dysplasia,not provided",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:9 LP:1",
"phenotype_combined": "Spondyloepiphyseal dysplasia congenita|not provided|14 conditions|Spondyloperipheral dysplasia|Spondyloepiphyseal dysplasia, Stanescu type;Spondyloperipheral dysplasia",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}