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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: 19-41988510-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=41988510&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 41988510,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000648268.1",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP1A3",
"gene_hgnc_id": 801,
"hgvs_c": "c.59G>A",
"hgvs_p": "p.Arg20Gln",
"transcript": "NM_152296.5",
"protein_id": "NP_689509.1",
"transcript_support_level": null,
"aa_start": 20,
"aa_end": null,
"aa_length": 1013,
"cds_start": 59,
"cds_end": null,
"cds_length": 3042,
"cdna_start": 213,
"cdna_end": null,
"cdna_length": 3551,
"mane_select": "ENST00000648268.1",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP1A3",
"gene_hgnc_id": 801,
"hgvs_c": "c.59G>A",
"hgvs_p": "p.Arg20Gln",
"transcript": "ENST00000648268.1",
"protein_id": "ENSP00000498113.1",
"transcript_support_level": null,
"aa_start": 20,
"aa_end": null,
"aa_length": 1013,
"cds_start": 59,
"cds_end": null,
"cds_length": 3042,
"cdna_start": 213,
"cdna_end": null,
"cdna_length": 3551,
"mane_select": "NM_152296.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000285505",
"gene_hgnc_id": null,
"hgvs_c": "n.59G>A",
"hgvs_p": null,
"transcript": "ENST00000644613.1",
"protein_id": "ENSP00000494711.1",
"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": 3536,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP1A3",
"gene_hgnc_id": 801,
"hgvs_c": "c.98G>A",
"hgvs_p": "p.Arg33Gln",
"transcript": "NM_001256214.2",
"protein_id": "NP_001243143.1",
"transcript_support_level": null,
"aa_start": 33,
"aa_end": null,
"aa_length": 1026,
"cds_start": 98,
"cds_end": null,
"cds_length": 3081,
"cdna_start": 252,
"cdna_end": null,
"cdna_length": 3590,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP1A3",
"gene_hgnc_id": 801,
"hgvs_c": "c.98G>A",
"hgvs_p": "p.Arg33Gln",
"transcript": "ENST00000545399.6",
"protein_id": "ENSP00000444688.1",
"transcript_support_level": 2,
"aa_start": 33,
"aa_end": null,
"aa_length": 1026,
"cds_start": 98,
"cds_end": null,
"cds_length": 3081,
"cdna_start": 292,
"cdna_end": null,
"cdna_length": 3628,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP1A3",
"gene_hgnc_id": 801,
"hgvs_c": "c.92G>A",
"hgvs_p": "p.Arg31Gln",
"transcript": "NM_001256213.2",
"protein_id": "NP_001243142.1",
"transcript_support_level": null,
"aa_start": 31,
"aa_end": null,
"aa_length": 1024,
"cds_start": 92,
"cds_end": null,
"cds_length": 3075,
"cdna_start": 128,
"cdna_end": null,
"cdna_length": 3466,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP1A3",
"gene_hgnc_id": 801,
"hgvs_c": "c.92G>A",
"hgvs_p": "p.Arg31Gln",
"transcript": "ENST00000543770.5",
"protein_id": "ENSP00000437577.1",
"transcript_support_level": 2,
"aa_start": 31,
"aa_end": null,
"aa_length": 1024,
"cds_start": 92,
"cds_end": null,
"cds_length": 3075,
"cdna_start": 128,
"cdna_end": null,
"cdna_length": 3427,
"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": 2,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP1A3",
"gene_hgnc_id": 801,
"hgvs_c": "n.59G>A",
"hgvs_p": null,
"transcript": "ENST00000441343.5",
"protein_id": "ENSP00000411503.1",
"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": 3818,
"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": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP1A3",
"gene_hgnc_id": 801,
"hgvs_c": "n.48G>A",
"hgvs_p": null,
"transcript": "ENST00000465007.1",
"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": 255,
"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": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP1A3",
"gene_hgnc_id": 801,
"hgvs_c": "n.368G>A",
"hgvs_p": null,
"transcript": "ENST00000468774.3",
"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": 603,
"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": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP1A3",
"gene_hgnc_id": 801,
"hgvs_c": "n.80G>A",
"hgvs_p": null,
"transcript": "ENST00000636258.1",
"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": 100,
"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": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP1A3",
"gene_hgnc_id": 801,
"hgvs_c": "n.81G>A",
"hgvs_p": null,
"transcript": "ENST00000636282.1",
"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": 100,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP1A3",
"gene_hgnc_id": 801,
"hgvs_c": "n.98G>A",
"hgvs_p": null,
"transcript": "ENST00000637406.1",
"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": 100,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP1A3",
"gene_hgnc_id": 801,
"hgvs_c": "c.-32G>A",
"hgvs_p": null,
"transcript": "ENST00000602133.5",
"protein_id": "ENSP00000471581.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 983,
"cds_start": -4,
"cds_end": null,
"cds_length": 2952,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3458,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP1A3",
"gene_hgnc_id": 801,
"hgvs_c": "c.-32G>A",
"hgvs_p": null,
"transcript": "ENST00000473086.3",
"protein_id": "ENSP00000469129.2",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 250,
"cds_start": -4,
"cds_end": null,
"cds_length": 754,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 889,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP1A3",
"gene_hgnc_id": 801,
"hgvs_c": "c.-32G>A",
"hgvs_p": null,
"transcript": "ENST00000636197.1",
"protein_id": "ENSP00000489877.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 0,
"cds_start": -4,
"cds_end": null,
"cds_length": 3,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 169,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP1A3",
"gene_hgnc_id": 801,
"hgvs_c": "c.-32G>A",
"hgvs_p": null,
"transcript": "XM_047438862.1",
"protein_id": "XP_047294818.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 983,
"cds_start": -4,
"cds_end": null,
"cds_length": 2952,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3410,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ATP1A3",
"gene_hgnc_id": 801,
"dbsnp": "rs949169436",
"frequency_reference_population": 0.000011152002,
"hom_count_reference_population": 1,
"allele_count_reference_population": 18,
"gnomad_exomes_af": 0.0000102607,
"gnomad_genomes_af": 0.0000197145,
"gnomad_exomes_ac": 15,
"gnomad_genomes_ac": 3,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.10024785995483398,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.169,
"revel_prediction": "Benign",
"alphamissense_score": 0.1373,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.18,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.86,
"phylop100way_prediction": "Benign",
"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": "Benign",
"acmg_criteria": "PP2,BP4_Moderate,BP6_Moderate,BS1",
"acmg_by_gene": [
{
"score": -7,
"benign_score": 8,
"pathogenic_score": 1,
"criteria": [
"PP2",
"BP4_Moderate",
"BP6_Moderate",
"BS1"
],
"verdict": "Benign",
"transcript": "ENST00000648268.1",
"gene_symbol": "ATP1A3",
"hgnc_id": 801,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.59G>A",
"hgvs_p": "p.Arg20Gln"
},
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate",
"BP6_Moderate"
],
"verdict": "Likely_benign",
"transcript": "ENST00000644613.1",
"gene_symbol": "ENSG00000285505",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.59G>A",
"hgvs_p": null
}
],
"clinvar_disease": "Dystonia 12",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "Dystonia 12",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}