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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: 4-15540994-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=15540994&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 15540994,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000424120.6",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 37,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CC2D2A",
"gene_hgnc_id": 29253,
"hgvs_c": "c.2161C>T",
"hgvs_p": "p.Pro721Ser",
"transcript": "NM_001378615.1",
"protein_id": "NP_001365544.1",
"transcript_support_level": null,
"aa_start": 721,
"aa_end": null,
"aa_length": 1620,
"cds_start": 2161,
"cds_end": null,
"cds_length": 4863,
"cdna_start": 2355,
"cdna_end": null,
"cdna_length": 5184,
"mane_select": "ENST00000424120.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 37,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CC2D2A",
"gene_hgnc_id": 29253,
"hgvs_c": "c.2161C>T",
"hgvs_p": "p.Pro721Ser",
"transcript": "ENST00000424120.6",
"protein_id": "ENSP00000403465.1",
"transcript_support_level": 5,
"aa_start": 721,
"aa_end": null,
"aa_length": 1620,
"cds_start": 2161,
"cds_end": null,
"cds_length": 4863,
"cdna_start": 2355,
"cdna_end": null,
"cdna_length": 5184,
"mane_select": "NM_001378615.1",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 38,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CC2D2A",
"gene_hgnc_id": 29253,
"hgvs_c": "c.2161C>T",
"hgvs_p": "p.Pro721Ser",
"transcript": "ENST00000503292.6",
"protein_id": "ENSP00000421809.1",
"transcript_support_level": 1,
"aa_start": 721,
"aa_end": null,
"aa_length": 1620,
"cds_start": 2161,
"cds_end": null,
"cds_length": 4863,
"cdna_start": 2400,
"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": 17,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CC2D2A",
"gene_hgnc_id": 29253,
"hgvs_c": "n.2341C>T",
"hgvs_p": null,
"transcript": "ENST00000513811.5",
"protein_id": null,
"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": 2744,
"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": 14,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CC2D2A",
"gene_hgnc_id": 29253,
"hgvs_c": "n.2014C>T",
"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": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 38,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CC2D2A",
"gene_hgnc_id": 29253,
"hgvs_c": "c.2161C>T",
"hgvs_p": "p.Pro721Ser",
"transcript": "ENST00000389652.11",
"protein_id": "ENSP00000374303.8",
"transcript_support_level": 5,
"aa_start": 721,
"aa_end": null,
"aa_length": 1632,
"cds_start": 2161,
"cds_end": null,
"cds_length": 4899,
"cdna_start": 2179,
"cdna_end": null,
"cdna_length": 5044,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 38,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CC2D2A",
"gene_hgnc_id": 29253,
"hgvs_c": "c.2161C>T",
"hgvs_p": "p.Pro721Ser",
"transcript": "NM_001080522.2",
"protein_id": "NP_001073991.2",
"transcript_support_level": null,
"aa_start": 721,
"aa_end": null,
"aa_length": 1620,
"cds_start": 2161,
"cds_end": null,
"cds_length": 4863,
"cdna_start": 2406,
"cdna_end": null,
"cdna_length": 5240,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CC2D2A",
"gene_hgnc_id": 29253,
"hgvs_c": "c.2014C>T",
"hgvs_p": "p.Pro672Ser",
"transcript": "NM_001378617.1",
"protein_id": "NP_001365546.1",
"transcript_support_level": null,
"aa_start": 672,
"aa_end": null,
"aa_length": 1571,
"cds_start": 2014,
"cds_end": null,
"cds_length": 4716,
"cdna_start": 2155,
"cdna_end": null,
"cdna_length": 4984,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CC2D2A",
"gene_hgnc_id": 29253,
"hgvs_c": "c.2014C>T",
"hgvs_p": "p.Pro672Ser",
"transcript": "ENST00000506643.5",
"protein_id": "ENSP00000422931.2",
"transcript_support_level": 2,
"aa_start": 672,
"aa_end": null,
"aa_length": 1571,
"cds_start": 2014,
"cds_end": null,
"cds_length": 4716,
"cdna_start": 2163,
"cdna_end": null,
"cdna_length": 4989,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CC2D2A",
"gene_hgnc_id": 29253,
"hgvs_c": "c.2014C>T",
"hgvs_p": "p.Pro672Ser",
"transcript": "ENST00000674945.1",
"protein_id": "ENSP00000502333.1",
"transcript_support_level": null,
"aa_start": 672,
"aa_end": null,
"aa_length": 1512,
"cds_start": 2014,
"cds_end": null,
"cds_length": 4539,
"cdna_start": 2163,
"cdna_end": null,
"cdna_length": 4809,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CC2D2A",
"gene_hgnc_id": 29253,
"hgvs_c": "c.2161C>T",
"hgvs_p": "p.Pro721Ser",
"transcript": "XM_011513872.4",
"protein_id": "XP_011512174.1",
"transcript_support_level": null,
"aa_start": 721,
"aa_end": null,
"aa_length": 1013,
"cds_start": 2161,
"cds_end": null,
"cds_length": 3042,
"cdna_start": 2372,
"cdna_end": null,
"cdna_length": 3362,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CC2D2A",
"gene_hgnc_id": 29253,
"hgvs_c": "c.2161C>T",
"hgvs_p": "p.Pro721Ser",
"transcript": "XM_047416010.1",
"protein_id": "XP_047271966.1",
"transcript_support_level": null,
"aa_start": 721,
"aa_end": null,
"aa_length": 1012,
"cds_start": 2161,
"cds_end": null,
"cds_length": 3039,
"cdna_start": 2372,
"cdna_end": null,
"cdna_length": 3379,
"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": 15,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CC2D2A",
"gene_hgnc_id": 29253,
"hgvs_c": "n.2014C>T",
"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": 2,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CC2D2A",
"gene_hgnc_id": 29253,
"hgvs_c": "n.240C>T",
"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": 17,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CC2D2A",
"gene_hgnc_id": 29253,
"hgvs_c": "n.2014C>T",
"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": 1,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CC2D2A",
"gene_hgnc_id": 29253,
"hgvs_c": "n.88C>T",
"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
}
],
"gene_symbol": "CC2D2A",
"gene_hgnc_id": 29253,
"dbsnp": "rs199768782",
"frequency_reference_population": 0.0015984048,
"hom_count_reference_population": 8,
"allele_count_reference_population": 2477,
"gnomad_exomes_af": 0.00165157,
"gnomad_genomes_af": 0.00111026,
"gnomad_exomes_ac": 2308,
"gnomad_genomes_ac": 169,
"gnomad_exomes_homalt": 8,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.03325304388999939,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.955,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9533,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.39,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.641,
"phylop100way_prediction": "Pathogenic",
"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": -12,
"acmg_classification": "Benign",
"acmg_criteria": "PP3,BP4_Strong,BP6,BS1,BS2",
"acmg_by_gene": [
{
"score": -12,
"benign_score": 13,
"pathogenic_score": 1,
"criteria": [
"PP3",
"BP4_Strong",
"BP6",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000424120.6",
"gene_symbol": "CC2D2A",
"hgnc_id": 29253,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2161C>T",
"hgvs_p": "p.Pro721Ser"
}
],
"clinvar_disease": " type 6,Joubert syndrome,Joubert syndrome 1,Meckel syndrome,Meckel-Gruber syndrome,not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:3 B:4",
"phenotype_combined": "not specified|Joubert syndrome;Meckel-Gruber syndrome|Joubert syndrome 1|Meckel syndrome, type 6|not provided",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}