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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: 17-40293507-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=40293507&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 9,
"criteria": [
"BP4_Strong",
"BP6",
"BS2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "CDC6",
"hgnc_id": 1744,
"hgvs_c": "c.712A>G",
"hgvs_p": "p.Thr238Ala",
"inheritance_mode": "AR,Unknown,AD",
"pathogenic_score": 0,
"score": -9,
"transcript": "NM_001254.4",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6,BS2",
"acmg_score": -9,
"allele_count_reference_population": 4947,
"alphamissense_prediction": null,
"alphamissense_score": 0.0883,
"alt": "G",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.52,
"chr": "17",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_disease": "Meier-Gorlin syndrome 5,not provided,not specified",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:2 LB:2",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.008472263813018799,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 560,
"aa_ref": "T",
"aa_start": 238,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4564,
"cdna_start": 937,
"cds_end": null,
"cds_length": 1683,
"cds_start": 712,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "NM_001254.4",
"gene_hgnc_id": 1744,
"gene_symbol": "CDC6",
"hgvs_c": "c.712A>G",
"hgvs_p": "p.Thr238Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000209728.9",
"protein_coding": true,
"protein_id": "NP_001245.1",
"strand": true,
"transcript": "NM_001254.4",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 560,
"aa_ref": "T",
"aa_start": 238,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 4564,
"cdna_start": 937,
"cds_end": null,
"cds_length": 1683,
"cds_start": 712,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000209728.9",
"gene_hgnc_id": 1744,
"gene_symbol": "CDC6",
"hgvs_c": "c.712A>G",
"hgvs_p": "p.Thr238Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001254.4",
"protein_coding": true,
"protein_id": "ENSP00000209728.4",
"strand": true,
"transcript": "ENST00000209728.9",
"transcript_support_level": 1
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 600,
"aa_ref": "T",
"aa_start": 238,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3519,
"cdna_start": 985,
"cds_end": null,
"cds_length": 1803,
"cds_start": 712,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000936767.1",
"gene_hgnc_id": 1744,
"gene_symbol": "CDC6",
"hgvs_c": "c.712A>G",
"hgvs_p": "p.Thr238Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000606826.1",
"strand": true,
"transcript": "ENST00000936767.1",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 569,
"aa_ref": "T",
"aa_start": 238,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2849,
"cdna_start": 933,
"cds_end": null,
"cds_length": 1710,
"cds_start": 712,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000936770.1",
"gene_hgnc_id": 1744,
"gene_symbol": "CDC6",
"hgvs_c": "c.712A>G",
"hgvs_p": "p.Thr238Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000606829.1",
"strand": true,
"transcript": "ENST00000936770.1",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 565,
"aa_ref": "T",
"aa_start": 238,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1938,
"cdna_start": 933,
"cds_end": null,
"cds_length": 1698,
"cds_start": 712,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000908721.1",
"gene_hgnc_id": 1744,
"gene_symbol": "CDC6",
"hgvs_c": "c.712A>G",
"hgvs_p": "p.Thr238Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000578780.1",
"strand": true,
"transcript": "ENST00000908721.1",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 560,
"aa_ref": "T",
"aa_start": 238,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1948,
"cdna_start": 742,
"cds_end": null,
"cds_length": 1683,
"cds_start": 712,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000649662.1",
"gene_hgnc_id": 1744,
"gene_symbol": "CDC6",
"hgvs_c": "c.712A>G",
"hgvs_p": "p.Thr238Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000497345.1",
"strand": true,
"transcript": "ENST00000649662.1",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 560,
"aa_ref": "T",
"aa_start": 238,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2859,
"cdna_start": 972,
"cds_end": null,
"cds_length": 1683,
"cds_start": 712,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000936769.1",
"gene_hgnc_id": 1744,
"gene_symbol": "CDC6",
"hgvs_c": "c.712A>G",
"hgvs_p": "p.Thr238Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000606828.1",
"strand": true,
"transcript": "ENST00000936769.1",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 559,
"aa_ref": "T",
"aa_start": 237,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2820,
"cdna_start": 934,
"cds_end": null,
"cds_length": 1680,
"cds_start": 709,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000908720.1",
"gene_hgnc_id": 1744,
"gene_symbol": "CDC6",
"hgvs_c": "c.709A>G",
"hgvs_p": "p.Thr237Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000578779.1",
"strand": true,
"transcript": "ENST00000908720.1",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 559,
"aa_ref": "T",
"aa_start": 238,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4592,
"cdna_start": 969,
"cds_end": null,
"cds_length": 1680,
"cds_start": 712,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000936766.1",
"gene_hgnc_id": 1744,
"gene_symbol": "CDC6",
"hgvs_c": "c.712A>G",
"hgvs_p": "p.Thr238Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000606825.1",
"strand": true,
"transcript": "ENST00000936766.1",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 559,
"aa_ref": "T",
"aa_start": 237,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2674,
"cdna_start": 788,
"cds_end": null,
"cds_length": 1680,
"cds_start": 709,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000936771.1",
"gene_hgnc_id": 1744,
"gene_symbol": "CDC6",
"hgvs_c": "c.709A>G",
"hgvs_p": "p.Thr237Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000606830.1",
"strand": true,
"transcript": "ENST00000936771.1",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 559,
"aa_ref": "T",
"aa_start": 238,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1891,
"cdna_start": 802,
"cds_end": null,
"cds_length": 1680,
"cds_start": 712,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000936774.1",
"gene_hgnc_id": 1744,
"gene_symbol": "CDC6",
"hgvs_c": "c.712A>G",
"hgvs_p": "p.Thr238Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000606833.1",
"strand": true,
"transcript": "ENST00000936774.1",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 548,
"aa_ref": "T",
"aa_start": 238,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2234,
"cdna_start": 952,
"cds_end": null,
"cds_length": 1647,
"cds_start": 712,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000936773.1",
"gene_hgnc_id": 1744,
"gene_symbol": "CDC6",
"hgvs_c": "c.712A>G",
"hgvs_p": "p.Thr238Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000606832.1",
"strand": true,
"transcript": "ENST00000936773.1",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 513,
"aa_ref": "T",
"aa_start": 238,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2637,
"cdna_start": 891,
"cds_end": null,
"cds_length": 1542,
"cds_start": 712,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000936772.1",
"gene_hgnc_id": 1744,
"gene_symbol": "CDC6",
"hgvs_c": "c.712A>G",
"hgvs_p": "p.Thr238Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000606831.1",
"strand": true,
"transcript": "ENST00000936772.1",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 485,
"aa_ref": "T",
"aa_start": 163,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2602,
"cdna_start": 713,
"cds_end": null,
"cds_length": 1458,
"cds_start": 487,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000936768.1",
"gene_hgnc_id": 1744,
"gene_symbol": "CDC6",
"hgvs_c": "c.487A>G",
"hgvs_p": "p.Thr163Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000606827.1",
"strand": true,
"transcript": "ENST00000936768.1",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 600,
"aa_ref": "T",
"aa_start": 238,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4684,
"cdna_start": 937,
"cds_end": null,
"cds_length": 1803,
"cds_start": 712,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "XM_011525541.3",
"gene_hgnc_id": 1744,
"gene_symbol": "CDC6",
"hgvs_c": "c.712A>G",
"hgvs_p": "p.Thr238Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011523843.1",
"strand": true,
"transcript": "XM_011525541.3",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 600,
"aa_ref": "T",
"aa_start": 238,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4726,
"cdna_start": 979,
"cds_end": null,
"cds_length": 1803,
"cds_start": 712,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "XM_011525542.2",
"gene_hgnc_id": 1744,
"gene_symbol": "CDC6",
"hgvs_c": "c.712A>G",
"hgvs_p": "p.Thr238Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011523844.1",
"strand": true,
"transcript": "XM_011525542.2",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 560,
"aa_ref": "T",
"aa_start": 238,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4606,
"cdna_start": 979,
"cds_end": null,
"cds_length": 1683,
"cds_start": 712,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "XM_047437207.1",
"gene_hgnc_id": 1744,
"gene_symbol": "CDC6",
"hgvs_c": "c.712A>G",
"hgvs_p": "p.Thr238Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047293163.1",
"strand": true,
"transcript": "XM_047437207.1",
"transcript_support_level": null
},
{
"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": 353,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000582402.1",
"gene_hgnc_id": 1744,
"gene_symbol": "CDC6",
"hgvs_c": "n.202+1839A>G",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000582402.1",
"transcript_support_level": 3
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs4135010",
"effect": "missense_variant",
"frequency_reference_population": 0.0030651013,
"gene_hgnc_id": 1744,
"gene_symbol": "CDC6",
"gnomad_exomes_ac": 4676,
"gnomad_exomes_af": 0.00319899,
"gnomad_exomes_homalt": 12,
"gnomad_genomes_ac": 271,
"gnomad_genomes_af": 0.0017798,
"gnomad_genomes_homalt": 1,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 13,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"phenotype_combined": "not specified|Meier-Gorlin syndrome 5|not provided",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 5.713,
"pos": 40293507,
"ref": "A",
"revel_prediction": "Benign",
"revel_score": 0.051,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_001254.4"
}
]
}