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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: 17-42564462-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=42564462&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "17",
"pos": 42564462,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_001042532.4",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COASY",
"gene_hgnc_id": 29932,
"hgvs_c": "c.932C>T",
"hgvs_p": "p.Ala311Val",
"transcript": "NM_025233.7",
"protein_id": "NP_079509.5",
"transcript_support_level": null,
"aa_start": 311,
"aa_end": null,
"aa_length": 564,
"cds_start": 932,
"cds_end": null,
"cds_length": 1695,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000393818.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_025233.7"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COASY",
"gene_hgnc_id": 29932,
"hgvs_c": "c.932C>T",
"hgvs_p": "p.Ala311Val",
"transcript": "ENST00000393818.3",
"protein_id": "ENSP00000377406.1",
"transcript_support_level": 1,
"aa_start": 311,
"aa_end": null,
"aa_length": 564,
"cds_start": 932,
"cds_end": null,
"cds_length": 1695,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_025233.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000393818.3"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COASY",
"gene_hgnc_id": 29932,
"hgvs_c": "c.1019C>T",
"hgvs_p": "p.Ala340Val",
"transcript": "ENST00000590958.5",
"protein_id": "ENSP00000464814.1",
"transcript_support_level": 1,
"aa_start": 340,
"aa_end": null,
"aa_length": 593,
"cds_start": 1019,
"cds_end": null,
"cds_length": 1782,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000590958.5"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COASY",
"gene_hgnc_id": 29932,
"hgvs_c": "c.932C>T",
"hgvs_p": "p.Ala311Val",
"transcript": "ENST00000421097.6",
"protein_id": "ENSP00000393564.2",
"transcript_support_level": 1,
"aa_start": 311,
"aa_end": null,
"aa_length": 564,
"cds_start": 932,
"cds_end": null,
"cds_length": 1695,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000421097.6"
},
{
"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": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COASY",
"gene_hgnc_id": 29932,
"hgvs_c": "n.1156C>T",
"hgvs_p": null,
"transcript": "ENST00000591753.1",
"protein_id": null,
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000591753.1"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COASY",
"gene_hgnc_id": 29932,
"hgvs_c": "c.1019C>T",
"hgvs_p": "p.Ala340Val",
"transcript": "NM_001042532.4",
"protein_id": "NP_001035997.2",
"transcript_support_level": null,
"aa_start": 340,
"aa_end": null,
"aa_length": 593,
"cds_start": 1019,
"cds_end": null,
"cds_length": 1782,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001042532.4"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COASY",
"gene_hgnc_id": 29932,
"hgvs_c": "c.932C>T",
"hgvs_p": "p.Ala311Val",
"transcript": "NM_001042529.3",
"protein_id": "NP_001035994.1",
"transcript_support_level": null,
"aa_start": 311,
"aa_end": null,
"aa_length": 564,
"cds_start": 932,
"cds_end": null,
"cds_length": 1695,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001042529.3"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COASY",
"gene_hgnc_id": 29932,
"hgvs_c": "c.47C>T",
"hgvs_p": "p.Ala16Val",
"transcript": "ENST00000591779.5",
"protein_id": "ENSP00000467687.1",
"transcript_support_level": 2,
"aa_start": 16,
"aa_end": null,
"aa_length": 114,
"cds_start": 47,
"cds_end": null,
"cds_length": 347,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000591779.5"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COASY",
"gene_hgnc_id": 29932,
"hgvs_c": "c.1019C>T",
"hgvs_p": "p.Ala340Val",
"transcript": "XM_006722116.5",
"protein_id": "XP_006722179.1",
"transcript_support_level": null,
"aa_start": 340,
"aa_end": null,
"aa_length": 593,
"cds_start": 1019,
"cds_end": null,
"cds_length": 1782,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_006722116.5"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COASY",
"gene_hgnc_id": 29932,
"hgvs_c": "c.932C>T",
"hgvs_p": "p.Ala311Val",
"transcript": "XM_011525300.2",
"protein_id": "XP_011523602.1",
"transcript_support_level": null,
"aa_start": 311,
"aa_end": null,
"aa_length": 564,
"cds_start": 932,
"cds_end": null,
"cds_length": 1695,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011525300.2"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COASY",
"gene_hgnc_id": 29932,
"hgvs_c": "c.932C>T",
"hgvs_p": "p.Ala311Val",
"transcript": "XM_047436849.1",
"protein_id": "XP_047292805.1",
"transcript_support_level": null,
"aa_start": 311,
"aa_end": null,
"aa_length": 466,
"cds_start": 932,
"cds_end": null,
"cds_length": 1401,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047436849.1"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COASY",
"gene_hgnc_id": 29932,
"hgvs_c": "c.932C>T",
"hgvs_p": "p.Ala311Val",
"transcript": "XM_047436850.1",
"protein_id": "XP_047292806.1",
"transcript_support_level": null,
"aa_start": 311,
"aa_end": null,
"aa_length": 362,
"cds_start": 932,
"cds_end": null,
"cds_length": 1089,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047436850.1"
},
{
"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": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COASY",
"gene_hgnc_id": 29932,
"hgvs_c": "n.178C>T",
"hgvs_p": null,
"transcript": "ENST00000588353.1",
"protein_id": null,
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000588353.1"
}
],
"gene_symbol": "COASY",
"gene_hgnc_id": 29932,
"dbsnp": "rs201949834",
"frequency_reference_population": 0.0003804246,
"hom_count_reference_population": 0,
"allele_count_reference_population": 614,
"gnomad_exomes_af": 0.000400863,
"gnomad_genomes_af": 0.000184041,
"gnomad_exomes_ac": 586,
"gnomad_genomes_ac": 28,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.07928940653800964,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.12999999523162842,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.243,
"revel_prediction": "Benign",
"alphamissense_score": 0.0904,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.25,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.252,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.13,
"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": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 2,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate"
],
"verdict": "Likely_benign",
"transcript": "NM_001042532.4",
"gene_symbol": "COASY",
"hgnc_id": 29932,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1019C>T",
"hgvs_p": "p.Ala340Val"
}
],
"clinvar_disease": "Neurodegeneration with brain iron accumulation 6,not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:2",
"phenotype_combined": "Neurodegeneration with brain iron accumulation 6|not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}