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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: 7-73704179-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=7&pos=73704179&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "7",
"pos": 73704179,
"ref": "G",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_004603.4",
"consequences": [
{
"aa_ref": "C",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STX1A",
"gene_hgnc_id": 11433,
"hgvs_c": "c.435C>G",
"hgvs_p": "p.Cys145Trp",
"transcript": "NM_004603.4",
"protein_id": "NP_004594.1",
"transcript_support_level": null,
"aa_start": 145,
"aa_end": null,
"aa_length": 288,
"cds_start": 435,
"cds_end": null,
"cds_length": 867,
"cdna_start": 473,
"cdna_end": null,
"cdna_length": 2102,
"mane_select": "ENST00000222812.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "W",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STX1A",
"gene_hgnc_id": 11433,
"hgvs_c": "c.435C>G",
"hgvs_p": "p.Cys145Trp",
"transcript": "ENST00000222812.8",
"protein_id": "ENSP00000222812.3",
"transcript_support_level": 1,
"aa_start": 145,
"aa_end": null,
"aa_length": 288,
"cds_start": 435,
"cds_end": null,
"cds_length": 867,
"cdna_start": 473,
"cdna_end": null,
"cdna_length": 2102,
"mane_select": "NM_004603.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STX1A",
"gene_hgnc_id": 11433,
"hgvs_c": "c.435C>G",
"hgvs_p": "p.Cys145Trp",
"transcript": "ENST00000395156.7",
"protein_id": "ENSP00000378585.3",
"transcript_support_level": 1,
"aa_start": 145,
"aa_end": null,
"aa_length": 251,
"cds_start": 435,
"cds_end": null,
"cds_length": 756,
"cdna_start": 463,
"cdna_end": null,
"cdna_length": 2050,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STX1A",
"gene_hgnc_id": 11433,
"hgvs_c": "c.435C>G",
"hgvs_p": "p.Cys145Trp",
"transcript": "ENST00000395154.7",
"protein_id": "ENSP00000378583.3",
"transcript_support_level": 3,
"aa_start": 145,
"aa_end": null,
"aa_length": 280,
"cds_start": 435,
"cds_end": null,
"cds_length": 843,
"cdna_start": 461,
"cdna_end": null,
"cdna_length": 1022,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STX1A",
"gene_hgnc_id": 11433,
"hgvs_c": "c.435C>G",
"hgvs_p": "p.Cys145Trp",
"transcript": "ENST00000395155.3",
"protein_id": "ENSP00000378584.3",
"transcript_support_level": 2,
"aa_start": 145,
"aa_end": null,
"aa_length": 260,
"cds_start": 435,
"cds_end": null,
"cds_length": 783,
"cdna_start": 435,
"cdna_end": null,
"cdna_length": 783,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STX1A",
"gene_hgnc_id": 11433,
"hgvs_c": "c.435C>G",
"hgvs_p": "p.Cys145Trp",
"transcript": "NM_001165903.2",
"protein_id": "NP_001159375.1",
"transcript_support_level": null,
"aa_start": 145,
"aa_end": null,
"aa_length": 251,
"cds_start": 435,
"cds_end": null,
"cds_length": 756,
"cdna_start": 473,
"cdna_end": null,
"cdna_length": 2056,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STX1A",
"gene_hgnc_id": 11433,
"hgvs_c": "c.435C>G",
"hgvs_p": "p.Cys145Trp",
"transcript": "XM_047420777.1",
"protein_id": "XP_047276733.1",
"transcript_support_level": null,
"aa_start": 145,
"aa_end": null,
"aa_length": 280,
"cds_start": 435,
"cds_end": null,
"cds_length": 843,
"cdna_start": 473,
"cdna_end": null,
"cdna_length": 1033,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STX1A",
"gene_hgnc_id": 11433,
"hgvs_c": "c.435C>G",
"hgvs_p": "p.Cys145Trp",
"transcript": "XM_047420778.1",
"protein_id": "XP_047276734.1",
"transcript_support_level": null,
"aa_start": 145,
"aa_end": null,
"aa_length": 260,
"cds_start": 435,
"cds_end": null,
"cds_length": 783,
"cdna_start": 473,
"cdna_end": null,
"cdna_length": 918,
"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": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STX1A",
"gene_hgnc_id": 11433,
"hgvs_c": "n.13C>G",
"hgvs_p": null,
"transcript": "ENST00000461441.5",
"protein_id": null,
"transcript_support_level": 4,
"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": 564,
"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": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STX1A",
"gene_hgnc_id": 11433,
"hgvs_c": "n.584C>G",
"hgvs_p": null,
"transcript": "ENST00000470878.5",
"protein_id": null,
"transcript_support_level": 3,
"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": 827,
"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": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STX1A",
"gene_hgnc_id": 11433,
"hgvs_c": "n.81C>G",
"hgvs_p": null,
"transcript": "ENST00000480126.5",
"protein_id": null,
"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": 724,
"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": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STX1A",
"gene_hgnc_id": 11433,
"hgvs_c": "n.318C>G",
"hgvs_p": null,
"transcript": "ENST00000491427.5",
"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": 710,
"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": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STX1A",
"gene_hgnc_id": 11433,
"hgvs_c": "n.468C>G",
"hgvs_p": null,
"transcript": "ENST00000494245.1",
"protein_id": null,
"transcript_support_level": 4,
"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": 565,
"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": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STX1A",
"gene_hgnc_id": 11433,
"hgvs_c": "n.344C>G",
"hgvs_p": null,
"transcript": "ENST00000496216.5",
"protein_id": null,
"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": 714,
"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": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "LOC105375350",
"gene_hgnc_id": null,
"hgvs_c": "n.437-653G>C",
"hgvs_p": null,
"transcript": "XR_927656.3",
"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": 793,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STX1A",
"gene_hgnc_id": 11433,
"hgvs_c": "n.-124C>G",
"hgvs_p": null,
"transcript": "ENST00000497980.5",
"protein_id": null,
"transcript_support_level": 3,
"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": 503,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STX1A",
"gene_hgnc_id": 11433,
"hgvs_c": "n.*1C>G",
"hgvs_p": null,
"transcript": "ENST00000462135.1",
"protein_id": null,
"transcript_support_level": 3,
"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": 568,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "STX1A",
"gene_hgnc_id": 11433,
"dbsnp": "rs200456346",
"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": 0.8423748016357422,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.547,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.9956,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.16,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 9.946,
"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": 7,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PP2,PP3_Moderate,PP5_Moderate",
"acmg_by_gene": [
{
"score": 7,
"benign_score": 0,
"pathogenic_score": 7,
"criteria": [
"PM2",
"PP2",
"PP3_Moderate",
"PP5_Moderate"
],
"verdict": "Likely_pathogenic",
"transcript": "NM_004603.4",
"gene_symbol": "STX1A",
"hgnc_id": 11433,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.435C>G",
"hgvs_p": "p.Cys145Trp"
},
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PM2",
"PP3_Moderate",
"PP5_Moderate"
],
"verdict": "Likely_pathogenic",
"transcript": "XR_927656.3",
"gene_symbol": "LOC105375350",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.437-653G>C",
"hgvs_p": null
}
],
"clinvar_disease": "Intellectual disability,Neurodevelopmental abnormality,Seizure",
"clinvar_classification": "Likely pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LP:1",
"phenotype_combined": "Neurodevelopmental abnormality|Intellectual disability;Seizure",
"pathogenicity_classification_combined": "Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}