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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: 6-45546940-A-AC (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=45546940&ref=A&alt=AC&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "6",
"pos": 45546940,
"ref": "A",
"alt": "AC",
"effect": "frameshift_variant",
"transcript": "ENST00000647337.2",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "P?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RUNX2",
"gene_hgnc_id": 10472,
"hgvs_c": "c.1205dupC",
"hgvs_p": "p.Pro403fs",
"transcript": "NM_001024630.4",
"protein_id": "NP_001019801.3",
"transcript_support_level": null,
"aa_start": 402,
"aa_end": null,
"aa_length": 521,
"cds_start": 1206,
"cds_end": null,
"cds_length": 1566,
"cdna_start": 1403,
"cdna_end": null,
"cdna_length": 5540,
"mane_select": "ENST00000647337.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P?",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RUNX2",
"gene_hgnc_id": 10472,
"hgvs_c": "c.1205dupC",
"hgvs_p": "p.Pro403fs",
"transcript": "ENST00000647337.2",
"protein_id": "ENSP00000495497.1",
"transcript_support_level": null,
"aa_start": 402,
"aa_end": null,
"aa_length": 521,
"cds_start": 1206,
"cds_end": null,
"cds_length": 1566,
"cdna_start": 1403,
"cdna_end": null,
"cdna_length": 5540,
"mane_select": "NM_001024630.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RUNX2",
"gene_hgnc_id": 10472,
"hgvs_c": "c.1163dupC",
"hgvs_p": "p.Pro389fs",
"transcript": "ENST00000359524.7",
"protein_id": "ENSP00000352514.5",
"transcript_support_level": 1,
"aa_start": 388,
"aa_end": null,
"aa_length": 507,
"cds_start": 1164,
"cds_end": null,
"cds_length": 1524,
"cdna_start": 1256,
"cdna_end": null,
"cdna_length": 5390,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RUNX2",
"gene_hgnc_id": 10472,
"hgvs_c": "c.1097dupC",
"hgvs_p": "p.Pro367fs",
"transcript": "ENST00000625924.1",
"protein_id": "ENSP00000485863.1",
"transcript_support_level": 1,
"aa_start": 366,
"aa_end": null,
"aa_length": 485,
"cds_start": 1098,
"cds_end": null,
"cds_length": 1458,
"cdna_start": 1098,
"cdna_end": null,
"cdna_length": 1458,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RUNX2",
"gene_hgnc_id": 10472,
"hgvs_c": "c.1205dupC",
"hgvs_p": "p.Pro403fs",
"transcript": "ENST00000371438.5",
"protein_id": "ENSP00000360493.1",
"transcript_support_level": 5,
"aa_start": 402,
"aa_end": null,
"aa_length": 521,
"cds_start": 1206,
"cds_end": null,
"cds_length": 1566,
"cdna_start": 1564,
"cdna_end": null,
"cdna_length": 5698,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RUNX2",
"gene_hgnc_id": 10472,
"hgvs_c": "c.1163dupC",
"hgvs_p": "p.Pro389fs",
"transcript": "NM_001369405.1",
"protein_id": "NP_001356334.1",
"transcript_support_level": null,
"aa_start": 388,
"aa_end": null,
"aa_length": 507,
"cds_start": 1164,
"cds_end": null,
"cds_length": 1524,
"cdna_start": 1466,
"cdna_end": null,
"cdna_length": 5603,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RUNX2",
"gene_hgnc_id": 10472,
"hgvs_c": "c.1139dupC",
"hgvs_p": "p.Pro381fs",
"transcript": "NM_001015051.4",
"protein_id": "NP_001015051.3",
"transcript_support_level": null,
"aa_start": 380,
"aa_end": null,
"aa_length": 499,
"cds_start": 1140,
"cds_end": null,
"cds_length": 1500,
"cdna_start": 1337,
"cdna_end": null,
"cdna_length": 5474,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RUNX2",
"gene_hgnc_id": 10472,
"hgvs_c": "c.1139dupC",
"hgvs_p": "p.Pro381fs",
"transcript": "ENST00000371432.7",
"protein_id": "ENSP00000360486.4",
"transcript_support_level": 5,
"aa_start": 380,
"aa_end": null,
"aa_length": 499,
"cds_start": 1140,
"cds_end": null,
"cds_length": 1500,
"cdna_start": 1350,
"cdna_end": null,
"cdna_length": 5487,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RUNX2",
"gene_hgnc_id": 10472,
"hgvs_c": "c.1139dupC",
"hgvs_p": "p.Pro381fs",
"transcript": "ENST00000371436.10",
"protein_id": "ENSP00000360491.6",
"transcript_support_level": 5,
"aa_start": 380,
"aa_end": null,
"aa_length": 499,
"cds_start": 1140,
"cds_end": null,
"cds_length": 1500,
"cdna_start": 1140,
"cdna_end": null,
"cdna_length": 1588,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RUNX2",
"gene_hgnc_id": 10472,
"hgvs_c": "c.1097dupC",
"hgvs_p": "p.Pro367fs",
"transcript": "NM_001278478.2",
"protein_id": "NP_001265407.1",
"transcript_support_level": null,
"aa_start": 366,
"aa_end": null,
"aa_length": 485,
"cds_start": 1098,
"cds_end": null,
"cds_length": 1458,
"cdna_start": 1400,
"cdna_end": null,
"cdna_length": 5537,
"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": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RUNX2",
"gene_hgnc_id": 10472,
"hgvs_c": "n.*726dupC",
"hgvs_p": null,
"transcript": "ENST00000483377.5",
"protein_id": "ENSP00000461357.1",
"transcript_support_level": 5,
"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": 1475,
"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": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RUNX2",
"gene_hgnc_id": 10472,
"hgvs_c": "n.*362dupC",
"hgvs_p": null,
"transcript": "ENST00000646519.1",
"protein_id": "ENSP00000496517.1",
"transcript_support_level": null,
"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": 5877,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RUNX2",
"gene_hgnc_id": 10472,
"hgvs_c": "n.*726dupC",
"hgvs_p": null,
"transcript": "ENST00000483377.5",
"protein_id": "ENSP00000461357.1",
"transcript_support_level": 5,
"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": 1475,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RUNX2",
"gene_hgnc_id": 10472,
"hgvs_c": "n.*362dupC",
"hgvs_p": null,
"transcript": "ENST00000646519.1",
"protein_id": "ENSP00000496517.1",
"transcript_support_level": null,
"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": 5877,
"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": 7,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "RUNX2",
"gene_hgnc_id": 10472,
"hgvs_c": "c.1021+34537dupC",
"hgvs_p": null,
"transcript": "ENST00000576263.5",
"protein_id": "ENSP00000458178.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 542,
"cds_start": -4,
"cds_end": null,
"cds_length": 1629,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2256,
"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": 6,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "RUNX2",
"gene_hgnc_id": 10472,
"hgvs_c": "n.*178+33291dupC",
"hgvs_p": null,
"transcript": "ENST00000478660.6",
"protein_id": "ENSP00000460188.1",
"transcript_support_level": 5,
"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": 2308,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "RUNX2",
"gene_hgnc_id": 10472,
"dbsnp": "rs730880314",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 5.772,
"phylop100way_prediction": "Uncertain_significance",
"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": 7,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PVS1_Strong,PM2,PP5",
"acmg_by_gene": [
{
"score": 7,
"benign_score": 0,
"pathogenic_score": 7,
"criteria": [
"PVS1_Strong",
"PM2",
"PP5"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000647337.2",
"gene_symbol": "RUNX2",
"hgnc_id": 10472,
"effects": [
"frameshift_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.1205dupC",
"hgvs_p": "p.Pro403fs"
}
],
"clinvar_disease": "Cleidocranial dysostosis",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "O:1",
"phenotype_combined": "Cleidocranial dysostosis",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}