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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: 4-15570411-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=15570411&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 15570411,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000424120.6",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 37,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CC2D2A",
"gene_hgnc_id": 29253,
"hgvs_c": "c.3509G>A",
"hgvs_p": "p.Arg1170Lys",
"transcript": "NM_001378615.1",
"protein_id": "NP_001365544.1",
"transcript_support_level": null,
"aa_start": 1170,
"aa_end": null,
"aa_length": 1620,
"cds_start": 3509,
"cds_end": null,
"cds_length": 4863,
"cdna_start": 3703,
"cdna_end": null,
"cdna_length": 5184,
"mane_select": "ENST00000424120.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "K",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 37,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CC2D2A",
"gene_hgnc_id": 29253,
"hgvs_c": "c.3509G>A",
"hgvs_p": "p.Arg1170Lys",
"transcript": "ENST00000424120.6",
"protein_id": "ENSP00000403465.1",
"transcript_support_level": 5,
"aa_start": 1170,
"aa_end": null,
"aa_length": 1620,
"cds_start": 3509,
"cds_end": null,
"cds_length": 4863,
"cdna_start": 3703,
"cdna_end": null,
"cdna_length": 5184,
"mane_select": "NM_001378615.1",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 38,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CC2D2A",
"gene_hgnc_id": 29253,
"hgvs_c": "c.3509G>A",
"hgvs_p": "p.Arg1170Lys",
"transcript": "ENST00000503292.6",
"protein_id": "ENSP00000421809.1",
"transcript_support_level": 1,
"aa_start": 1170,
"aa_end": null,
"aa_length": 1620,
"cds_start": 3509,
"cds_end": null,
"cds_length": 4863,
"cdna_start": 3748,
"cdna_end": null,
"cdna_length": 5226,
"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": 25,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CC2D2A",
"gene_hgnc_id": 29253,
"hgvs_c": "n.3362G>A",
"hgvs_p": null,
"transcript": "ENST00000634028.2",
"protein_id": "ENSP00000488669.2",
"transcript_support_level": 1,
"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": 4784,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 38,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CC2D2A",
"gene_hgnc_id": 29253,
"hgvs_c": "c.3524G>A",
"hgvs_p": "p.Arg1175Lys",
"transcript": "ENST00000389652.11",
"protein_id": "ENSP00000374303.8",
"transcript_support_level": 5,
"aa_start": 1175,
"aa_end": null,
"aa_length": 1632,
"cds_start": 3524,
"cds_end": null,
"cds_length": 4899,
"cdna_start": 3542,
"cdna_end": null,
"cdna_length": 5044,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 38,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CC2D2A",
"gene_hgnc_id": 29253,
"hgvs_c": "c.3509G>A",
"hgvs_p": "p.Arg1170Lys",
"transcript": "NM_001080522.2",
"protein_id": "NP_001073991.2",
"transcript_support_level": null,
"aa_start": 1170,
"aa_end": null,
"aa_length": 1620,
"cds_start": 3509,
"cds_end": null,
"cds_length": 4863,
"cdna_start": 3754,
"cdna_end": null,
"cdna_length": 5240,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CC2D2A",
"gene_hgnc_id": 29253,
"hgvs_c": "c.3362G>A",
"hgvs_p": "p.Arg1121Lys",
"transcript": "NM_001378617.1",
"protein_id": "NP_001365546.1",
"transcript_support_level": null,
"aa_start": 1121,
"aa_end": null,
"aa_length": 1571,
"cds_start": 3362,
"cds_end": null,
"cds_length": 4716,
"cdna_start": 3503,
"cdna_end": null,
"cdna_length": 4984,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CC2D2A",
"gene_hgnc_id": 29253,
"hgvs_c": "c.3362G>A",
"hgvs_p": "p.Arg1121Lys",
"transcript": "ENST00000506643.5",
"protein_id": "ENSP00000422931.2",
"transcript_support_level": 2,
"aa_start": 1121,
"aa_end": null,
"aa_length": 1571,
"cds_start": 3362,
"cds_end": null,
"cds_length": 4716,
"cdna_start": 3511,
"cdna_end": null,
"cdna_length": 4989,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CC2D2A",
"gene_hgnc_id": 29253,
"hgvs_c": "c.3362G>A",
"hgvs_p": "p.Arg1121Lys",
"transcript": "ENST00000674945.1",
"protein_id": "ENSP00000502333.1",
"transcript_support_level": null,
"aa_start": 1121,
"aa_end": null,
"aa_length": 1512,
"cds_start": 3362,
"cds_end": null,
"cds_length": 4539,
"cdna_start": 3511,
"cdna_end": null,
"cdna_length": 4809,
"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": 26,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CC2D2A",
"gene_hgnc_id": 29253,
"hgvs_c": "n.*515G>A",
"hgvs_p": null,
"transcript": "ENST00000650860.2",
"protein_id": "ENSP00000498775.1",
"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": 5513,
"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": 12,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CC2D2A",
"gene_hgnc_id": 29253,
"hgvs_c": "n.4320G>A",
"hgvs_p": null,
"transcript": "ENST00000675619.1",
"protein_id": null,
"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": 4929,
"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": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CC2D2A",
"gene_hgnc_id": 29253,
"hgvs_c": "n.729G>A",
"hgvs_p": null,
"transcript": "ENST00000675768.1",
"protein_id": null,
"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": 2447,
"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": 28,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CC2D2A",
"gene_hgnc_id": 29253,
"hgvs_c": "n.*515G>A",
"hgvs_p": null,
"transcript": "ENST00000676337.1",
"protein_id": "ENSP00000501728.1",
"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": 4588,
"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": 11,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CC2D2A",
"gene_hgnc_id": 29253,
"hgvs_c": "n.4168G>A",
"hgvs_p": null,
"transcript": "ENST00000680586.1",
"protein_id": null,
"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": 6514,
"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": 26,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CC2D2A",
"gene_hgnc_id": 29253,
"hgvs_c": "n.*515G>A",
"hgvs_p": null,
"transcript": "ENST00000650860.2",
"protein_id": "ENSP00000498775.1",
"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": 5513,
"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": 28,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CC2D2A",
"gene_hgnc_id": 29253,
"hgvs_c": "n.*515G>A",
"hgvs_p": null,
"transcript": "ENST00000676337.1",
"protein_id": "ENSP00000501728.1",
"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": 4588,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "LOC124900671",
"gene_hgnc_id": null,
"hgvs_c": "n.130+320C>T",
"hgvs_p": null,
"transcript": "XR_007058061.1",
"protein_id": null,
"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": 629,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "CC2D2A",
"gene_hgnc_id": 29253,
"dbsnp": "rs61734948",
"frequency_reference_population": 0.0011578777,
"hom_count_reference_population": 25,
"allele_count_reference_population": 1852,
"gnomad_exomes_af": 0.000639176,
"gnomad_genomes_af": 0.00608659,
"gnomad_exomes_ac": 925,
"gnomad_genomes_ac": 927,
"gnomad_exomes_homalt": 13,
"gnomad_genomes_homalt": 12,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.009373515844345093,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.527,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.1222,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.08,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 7.234,
"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": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BS1,BS2",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000424120.6",
"gene_symbol": "CC2D2A",
"hgnc_id": 29253,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.3509G>A",
"hgvs_p": "p.Arg1170Lys"
},
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "XR_007058061.1",
"gene_symbol": "LOC124900671",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.130+320C>T",
"hgvs_p": null
}
],
"clinvar_disease": " type 6,Joubert syndrome,Joubert syndrome 9,Meckel syndrome,Meckel-Gruber syndrome,not provided,not specified",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:2 B:4",
"phenotype_combined": "not specified|Joubert syndrome;Meckel-Gruber syndrome|Joubert syndrome 9|Meckel syndrome, type 6|not provided",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}