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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: 19-41982102-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=41982102&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM1",
"PM2",
"PP2",
"PP3_Strong",
"PP5_Moderate"
],
"effects": [
"missense_variant"
],
"gene_symbol": "ATP1A3",
"hgnc_id": 801,
"hgvs_c": "c.1037G>A",
"hgvs_p": "p.Cys346Tyr",
"inheritance_mode": "AD,AR",
"pathogenic_score": 11,
"score": 11,
"transcript": "NM_001256214.2",
"verdict": "Pathogenic"
},
{
"benign_score": 0,
"criteria": [
"PM2",
"PP3_Strong",
"PP5_Moderate"
],
"effects": [
"non_coding_transcript_exon_variant"
],
"gene_symbol": "ENSG00000285505",
"hgnc_id": null,
"hgvs_c": "n.998G>A",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 8,
"score": 8,
"transcript": "ENST00000644613.1",
"verdict": "Likely_pathogenic"
}
],
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM1,PM2,PP2,PP3_Strong,PP5_Moderate",
"acmg_score": 11,
"allele_count_reference_population": 0,
"alphamissense_prediction": null,
"alphamissense_score": 0.9957,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.44,
"chr": "19",
"clinvar_classification": "Likely pathogenic",
"clinvar_disease": "Alternating hemiplegia of childhood",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LP:1",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.9555726051330566,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 1013,
"aa_ref": "C",
"aa_start": 333,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3551,
"cdna_start": 1152,
"cds_end": null,
"cds_length": 3042,
"cds_start": 998,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "NM_152296.5",
"gene_hgnc_id": 801,
"gene_symbol": "ATP1A3",
"hgvs_c": "c.998G>A",
"hgvs_p": "p.Cys333Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000648268.1",
"protein_coding": true,
"protein_id": "NP_689509.1",
"strand": false,
"transcript": "NM_152296.5",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 1013,
"aa_ref": "C",
"aa_start": 333,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 3551,
"cdna_start": 1152,
"cds_end": null,
"cds_length": 3042,
"cds_start": 998,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000648268.1",
"gene_hgnc_id": 801,
"gene_symbol": "ATP1A3",
"hgvs_c": "c.998G>A",
"hgvs_p": "p.Cys333Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_152296.5",
"protein_coding": true,
"protein_id": "ENSP00000498113.1",
"strand": false,
"transcript": "ENST00000648268.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": true,
"cdna_end": null,
"cdna_length": 3536,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 25,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000644613.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000285505",
"hgvs_c": "n.998G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000494711.1",
"strand": false,
"transcript": "ENST00000644613.1",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 1026,
"aa_ref": "C",
"aa_start": 346,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3590,
"cdna_start": 1191,
"cds_end": null,
"cds_length": 3081,
"cds_start": 1037,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "NM_001256214.2",
"gene_hgnc_id": 801,
"gene_symbol": "ATP1A3",
"hgvs_c": "c.1037G>A",
"hgvs_p": "p.Cys346Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001243143.1",
"strand": false,
"transcript": "NM_001256214.2",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 1026,
"aa_ref": "C",
"aa_start": 346,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3628,
"cdna_start": 1231,
"cds_end": null,
"cds_length": 3081,
"cds_start": 1037,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000545399.6",
"gene_hgnc_id": 801,
"gene_symbol": "ATP1A3",
"hgvs_c": "c.1037G>A",
"hgvs_p": "p.Cys346Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000444688.1",
"strand": false,
"transcript": "ENST00000545399.6",
"transcript_support_level": 2
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 1024,
"aa_ref": "C",
"aa_start": 344,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3466,
"cdna_start": 1067,
"cds_end": null,
"cds_length": 3075,
"cds_start": 1031,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "NM_001256213.2",
"gene_hgnc_id": 801,
"gene_symbol": "ATP1A3",
"hgvs_c": "c.1031G>A",
"hgvs_p": "p.Cys344Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001243142.1",
"strand": false,
"transcript": "NM_001256213.2",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 1024,
"aa_ref": "C",
"aa_start": 344,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3427,
"cdna_start": 1067,
"cds_end": null,
"cds_length": 3075,
"cds_start": 1031,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000543770.5",
"gene_hgnc_id": 801,
"gene_symbol": "ATP1A3",
"hgvs_c": "c.1031G>A",
"hgvs_p": "p.Cys344Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000437577.1",
"strand": false,
"transcript": "ENST00000543770.5",
"transcript_support_level": 2
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 996,
"aa_ref": "C",
"aa_start": 333,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3502,
"cdna_start": 1154,
"cds_end": null,
"cds_length": 2991,
"cds_start": 998,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000890880.1",
"gene_hgnc_id": 801,
"gene_symbol": "ATP1A3",
"hgvs_c": "c.998G>A",
"hgvs_p": "p.Cys333Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000560939.1",
"strand": false,
"transcript": "ENST00000890880.1",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 994,
"aa_ref": "C",
"aa_start": 333,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3494,
"cdna_start": 1152,
"cds_end": null,
"cds_length": 2985,
"cds_start": 998,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000890884.1",
"gene_hgnc_id": 801,
"gene_symbol": "ATP1A3",
"hgvs_c": "c.998G>A",
"hgvs_p": "p.Cys333Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000560943.1",
"strand": false,
"transcript": "ENST00000890884.1",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 984,
"aa_ref": "C",
"aa_start": 333,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3330,
"cdna_start": 1018,
"cds_end": null,
"cds_length": 2955,
"cds_start": 998,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000919566.1",
"gene_hgnc_id": 801,
"gene_symbol": "ATP1A3",
"hgvs_c": "c.998G>A",
"hgvs_p": "p.Cys333Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000589625.1",
"strand": false,
"transcript": "ENST00000919566.1",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 983,
"aa_ref": "C",
"aa_start": 303,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3458,
"cdna_start": 1061,
"cds_end": null,
"cds_length": 2952,
"cds_start": 908,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000602133.5",
"gene_hgnc_id": 801,
"gene_symbol": "ATP1A3",
"hgvs_c": "c.908G>A",
"hgvs_p": "p.Cys303Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000471581.1",
"strand": false,
"transcript": "ENST00000602133.5",
"transcript_support_level": 2
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 945,
"aa_ref": "C",
"aa_start": 265,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3347,
"cdna_start": 948,
"cds_end": null,
"cds_length": 2838,
"cds_start": 794,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000890882.1",
"gene_hgnc_id": 801,
"gene_symbol": "ATP1A3",
"hgvs_c": "c.794G>A",
"hgvs_p": "p.Cys265Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000560941.1",
"strand": false,
"transcript": "ENST00000890882.1",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 842,
"aa_ref": "C",
"aa_start": 162,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3034,
"cdna_start": 637,
"cds_end": null,
"cds_length": 2529,
"cds_start": 485,
"consequences": [
"missense_variant"
],
"exon_count": 19,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000948333.1",
"gene_hgnc_id": 801,
"gene_symbol": "ATP1A3",
"hgvs_c": "c.485G>A",
"hgvs_p": "p.Cys162Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000618392.1",
"strand": false,
"transcript": "ENST00000948333.1",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 983,
"aa_ref": "C",
"aa_start": 303,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3410,
"cdna_start": 1011,
"cds_end": null,
"cds_length": 2952,
"cds_start": 908,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "XM_047438862.1",
"gene_hgnc_id": 801,
"gene_symbol": "ATP1A3",
"hgvs_c": "c.908G>A",
"hgvs_p": "p.Cys303Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047294818.1",
"strand": false,
"transcript": "XM_047438862.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "non_stop_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 3818,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 22,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000441343.5",
"gene_hgnc_id": 801,
"gene_symbol": "ATP1A3",
"hgvs_c": "n.998G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000411503.1",
"strand": false,
"transcript": "ENST00000441343.5",
"transcript_support_level": 2
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs606231430",
"effect": "missense_variant",
"frequency_reference_population": null,
"gene_hgnc_id": 801,
"gene_symbol": "ATP1A3",
"gnomad_exomes_ac": null,
"gnomad_exomes_af": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Likely pathogenic",
"phenotype_combined": "Alternating hemiplegia of childhood",
"phylop100way_prediction": "Pathogenic",
"phylop100way_score": 7.879,
"pos": 41982102,
"ref": "C",
"revel_prediction": "Pathogenic",
"revel_score": 0.94,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_001256214.2"
}
]
}