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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: 19-41986224-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=41986224&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 41986224,
"ref": "G",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "ENST00000648268.1",
"consequences": [
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP1A3",
"gene_hgnc_id": 801,
"hgvs_c": "c.363C>T",
"hgvs_p": "p.Tyr121Tyr",
"transcript": "NM_152296.5",
"protein_id": "NP_689509.1",
"transcript_support_level": null,
"aa_start": 121,
"aa_end": null,
"aa_length": 1013,
"cds_start": 363,
"cds_end": null,
"cds_length": 3042,
"cdna_start": 517,
"cdna_end": null,
"cdna_length": 3551,
"mane_select": "ENST00000648268.1",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP1A3",
"gene_hgnc_id": 801,
"hgvs_c": "c.363C>T",
"hgvs_p": "p.Tyr121Tyr",
"transcript": "ENST00000648268.1",
"protein_id": "ENSP00000498113.1",
"transcript_support_level": null,
"aa_start": 121,
"aa_end": null,
"aa_length": 1013,
"cds_start": 363,
"cds_end": null,
"cds_length": 3042,
"cdna_start": 517,
"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": 5,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000285505",
"gene_hgnc_id": null,
"hgvs_c": "n.363C>T",
"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": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP1A3",
"gene_hgnc_id": 801,
"hgvs_c": "c.402C>T",
"hgvs_p": "p.Tyr134Tyr",
"transcript": "NM_001256214.2",
"protein_id": "NP_001243143.1",
"transcript_support_level": null,
"aa_start": 134,
"aa_end": null,
"aa_length": 1026,
"cds_start": 402,
"cds_end": null,
"cds_length": 3081,
"cdna_start": 556,
"cdna_end": null,
"cdna_length": 3590,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP1A3",
"gene_hgnc_id": 801,
"hgvs_c": "c.402C>T",
"hgvs_p": "p.Tyr134Tyr",
"transcript": "ENST00000545399.6",
"protein_id": "ENSP00000444688.1",
"transcript_support_level": 2,
"aa_start": 134,
"aa_end": null,
"aa_length": 1026,
"cds_start": 402,
"cds_end": null,
"cds_length": 3081,
"cdna_start": 596,
"cdna_end": null,
"cdna_length": 3628,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP1A3",
"gene_hgnc_id": 801,
"hgvs_c": "c.396C>T",
"hgvs_p": "p.Tyr132Tyr",
"transcript": "NM_001256213.2",
"protein_id": "NP_001243142.1",
"transcript_support_level": null,
"aa_start": 132,
"aa_end": null,
"aa_length": 1024,
"cds_start": 396,
"cds_end": null,
"cds_length": 3075,
"cdna_start": 432,
"cdna_end": null,
"cdna_length": 3466,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP1A3",
"gene_hgnc_id": 801,
"hgvs_c": "c.396C>T",
"hgvs_p": "p.Tyr132Tyr",
"transcript": "ENST00000543770.5",
"protein_id": "ENSP00000437577.1",
"transcript_support_level": 2,
"aa_start": 132,
"aa_end": null,
"aa_length": 1024,
"cds_start": 396,
"cds_end": null,
"cds_length": 3075,
"cdna_start": 432,
"cdna_end": null,
"cdna_length": 3427,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP1A3",
"gene_hgnc_id": 801,
"hgvs_c": "c.273C>T",
"hgvs_p": "p.Tyr91Tyr",
"transcript": "ENST00000602133.5",
"protein_id": "ENSP00000471581.1",
"transcript_support_level": 2,
"aa_start": 91,
"aa_end": null,
"aa_length": 983,
"cds_start": 273,
"cds_end": null,
"cds_length": 2952,
"cdna_start": 426,
"cdna_end": null,
"cdna_length": 3458,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP1A3",
"gene_hgnc_id": 801,
"hgvs_c": "c.273C>T",
"hgvs_p": "p.Tyr91Tyr",
"transcript": "ENST00000473086.3",
"protein_id": "ENSP00000469129.2",
"transcript_support_level": 5,
"aa_start": 91,
"aa_end": null,
"aa_length": 250,
"cds_start": 273,
"cds_end": null,
"cds_length": 754,
"cdna_start": 408,
"cdna_end": null,
"cdna_length": 889,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP1A3",
"gene_hgnc_id": 801,
"hgvs_c": "c.273C>T",
"hgvs_p": "p.Tyr91Tyr",
"transcript": "XM_047438862.1",
"protein_id": "XP_047294818.1",
"transcript_support_level": null,
"aa_start": 91,
"aa_end": null,
"aa_length": 983,
"cds_start": 273,
"cds_end": null,
"cds_length": 2952,
"cdna_start": 376,
"cdna_end": null,
"cdna_length": 3410,
"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": 5,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP1A3",
"gene_hgnc_id": 801,
"hgvs_c": "n.363C>T",
"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.478C>T",
"hgvs_p": null,
"transcript": "ENST00000645448.1",
"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": 1052,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ATP1A3",
"gene_hgnc_id": 801,
"dbsnp": "rs373180830",
"frequency_reference_population": 0.00031228855,
"hom_count_reference_population": 4,
"allele_count_reference_population": 504,
"gnomad_exomes_af": 0.000329072,
"gnomad_genomes_af": 0.000151109,
"gnomad_exomes_ac": 481,
"gnomad_genomes_ac": 23,
"gnomad_exomes_homalt": 4,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.5600000023841858,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.56,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.88,
"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": -21,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BS1,BS2",
"acmg_by_gene": [
{
"score": -21,
"benign_score": 21,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000648268.1",
"gene_symbol": "ATP1A3",
"hgnc_id": 801,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.363C>T",
"hgvs_p": "p.Tyr121Tyr"
},
{
"score": -16,
"benign_score": 16,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000644613.1",
"gene_symbol": "ENSG00000285505",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.363C>T",
"hgvs_p": null
}
],
"clinvar_disease": "ATP1A3-related disorder,Alternating hemiplegia of childhood 2,Cerebellar ataxia-areflexia-pes cavus-optic atrophy-sensorineural hearing loss syndrome,Developmental and epileptic encephalopathy 99,Dystonia 12,not provided,not specified",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:1 B:8",
"phenotype_combined": "Alternating hemiplegia of childhood 2|Dystonia 12|not provided|Cerebellar ataxia-areflexia-pes cavus-optic atrophy-sensorineural hearing loss syndrome|Developmental and epileptic encephalopathy 99|not specified|ATP1A3-related disorder",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}