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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: 19-41967744-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=41967744&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 41967744,
"ref": "C",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000648268.1",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP1A3",
"gene_hgnc_id": 801,
"hgvs_c": "c.2839G>C",
"hgvs_p": "p.Gly947Arg",
"transcript": "NM_152296.5",
"protein_id": "NP_689509.1",
"transcript_support_level": null,
"aa_start": 947,
"aa_end": null,
"aa_length": 1013,
"cds_start": 2839,
"cds_end": null,
"cds_length": 3042,
"cdna_start": 2993,
"cdna_end": null,
"cdna_length": 3551,
"mane_select": "ENST00000648268.1",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP1A3",
"gene_hgnc_id": 801,
"hgvs_c": "c.2839G>C",
"hgvs_p": "p.Gly947Arg",
"transcript": "ENST00000648268.1",
"protein_id": "ENSP00000498113.1",
"transcript_support_level": null,
"aa_start": 947,
"aa_end": null,
"aa_length": 1013,
"cds_start": 2839,
"cds_end": null,
"cds_length": 3042,
"cdna_start": 2993,
"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": 21,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000285505",
"gene_hgnc_id": null,
"hgvs_c": "n.2839G>C",
"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": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP1A3",
"gene_hgnc_id": 801,
"hgvs_c": "c.2878G>C",
"hgvs_p": "p.Gly960Arg",
"transcript": "NM_001256214.2",
"protein_id": "NP_001243143.1",
"transcript_support_level": null,
"aa_start": 960,
"aa_end": null,
"aa_length": 1026,
"cds_start": 2878,
"cds_end": null,
"cds_length": 3081,
"cdna_start": 3032,
"cdna_end": null,
"cdna_length": 3590,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP1A3",
"gene_hgnc_id": 801,
"hgvs_c": "c.2878G>C",
"hgvs_p": "p.Gly960Arg",
"transcript": "ENST00000545399.6",
"protein_id": "ENSP00000444688.1",
"transcript_support_level": 2,
"aa_start": 960,
"aa_end": null,
"aa_length": 1026,
"cds_start": 2878,
"cds_end": null,
"cds_length": 3081,
"cdna_start": 3072,
"cdna_end": null,
"cdna_length": 3628,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP1A3",
"gene_hgnc_id": 801,
"hgvs_c": "c.2872G>C",
"hgvs_p": "p.Gly958Arg",
"transcript": "NM_001256213.2",
"protein_id": "NP_001243142.1",
"transcript_support_level": null,
"aa_start": 958,
"aa_end": null,
"aa_length": 1024,
"cds_start": 2872,
"cds_end": null,
"cds_length": 3075,
"cdna_start": 2908,
"cdna_end": null,
"cdna_length": 3466,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP1A3",
"gene_hgnc_id": 801,
"hgvs_c": "c.2872G>C",
"hgvs_p": "p.Gly958Arg",
"transcript": "ENST00000543770.5",
"protein_id": "ENSP00000437577.1",
"transcript_support_level": 2,
"aa_start": 958,
"aa_end": null,
"aa_length": 1024,
"cds_start": 2872,
"cds_end": null,
"cds_length": 3075,
"cdna_start": 2908,
"cdna_end": null,
"cdna_length": 3427,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP1A3",
"gene_hgnc_id": 801,
"hgvs_c": "c.2749G>C",
"hgvs_p": "p.Gly917Arg",
"transcript": "ENST00000602133.5",
"protein_id": "ENSP00000471581.1",
"transcript_support_level": 2,
"aa_start": 917,
"aa_end": null,
"aa_length": 983,
"cds_start": 2749,
"cds_end": null,
"cds_length": 2952,
"cdna_start": 2902,
"cdna_end": null,
"cdna_length": 3458,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP1A3",
"gene_hgnc_id": 801,
"hgvs_c": "c.2749G>C",
"hgvs_p": "p.Gly917Arg",
"transcript": "XM_047438862.1",
"protein_id": "XP_047294818.1",
"transcript_support_level": null,
"aa_start": 917,
"aa_end": null,
"aa_length": 983,
"cds_start": 2749,
"cds_end": null,
"cds_length": 2952,
"cdna_start": 2852,
"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": 21,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP1A3",
"gene_hgnc_id": 801,
"hgvs_c": "n.2839G>C",
"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
}
],
"gene_symbol": "ATP1A3",
"gene_hgnc_id": 801,
"dbsnp": "rs398122887",
"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": 0.9751735925674438,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.97,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9991,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.57,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.897,
"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": 19,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PS1_Very_Strong,PM2,PM5,PP2,PP3_Strong,PP5_Moderate",
"acmg_by_gene": [
{
"score": 19,
"benign_score": 0,
"pathogenic_score": 19,
"criteria": [
"PS1_Very_Strong",
"PM2",
"PM5",
"PP2",
"PP3_Strong",
"PP5_Moderate"
],
"verdict": "Pathogenic",
"transcript": "ENST00000648268.1",
"gene_symbol": "ATP1A3",
"hgnc_id": 801,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.2839G>C",
"hgvs_p": "p.Gly947Arg"
},
{
"score": 8,
"benign_score": 0,
"pathogenic_score": 8,
"criteria": [
"PM2",
"PP3_Strong",
"PP5_Moderate"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000644613.1",
"gene_symbol": "ENSG00000285505",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.2839G>C",
"hgvs_p": null
}
],
"clinvar_disease": "Alternating hemiplegia of childhood 2,Dystonia 12",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "P:1 O:1",
"phenotype_combined": "Alternating hemiplegia of childhood 2|Dystonia 12",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}