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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: 19-41970395-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=41970395&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM1",
"PM2",
"PP2",
"PP3_Strong"
],
"effects": [
"missense_variant"
],
"gene_symbol": "ATP1A3",
"hgnc_id": 801,
"hgvs_c": "c.2450C>T",
"hgvs_p": "p.Thr817Ile",
"inheritance_mode": "AD,AR",
"pathogenic_score": 9,
"score": 9,
"transcript": "NM_001256214.2",
"verdict": "Likely_pathogenic"
},
{
"benign_score": 0,
"criteria": [
"PM2",
"PP3_Strong"
],
"effects": [
"non_coding_transcript_exon_variant"
],
"gene_symbol": "ENSG00000285505",
"hgnc_id": null,
"hgvs_c": "n.2411C>T",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 6,
"score": 6,
"transcript": "ENST00000644613.1",
"verdict": "Likely_pathogenic"
}
],
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM1,PM2,PP2,PP3_Strong",
"acmg_score": 9,
"allele_count_reference_population": 0,
"alphamissense_prediction": null,
"alphamissense_score": 0.9986,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.51,
"chr": "19",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.9630776643753052,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 1013,
"aa_ref": "T",
"aa_start": 804,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3551,
"cdna_start": 2565,
"cds_end": null,
"cds_length": 3042,
"cds_start": 2411,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "NM_152296.5",
"gene_hgnc_id": 801,
"gene_symbol": "ATP1A3",
"hgvs_c": "c.2411C>T",
"hgvs_p": "p.Thr804Ile",
"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": "I",
"aa_end": null,
"aa_length": 1013,
"aa_ref": "T",
"aa_start": 804,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 3551,
"cdna_start": 2565,
"cds_end": null,
"cds_length": 3042,
"cds_start": 2411,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "ENST00000648268.1",
"gene_hgnc_id": 801,
"gene_symbol": "ATP1A3",
"hgvs_c": "c.2411C>T",
"hgvs_p": "p.Thr804Ile",
"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": 17,
"exon_rank_end": null,
"feature": "ENST00000644613.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000285505",
"hgvs_c": "n.2411C>T",
"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": "I",
"aa_end": null,
"aa_length": 1026,
"aa_ref": "T",
"aa_start": 817,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3590,
"cdna_start": 2604,
"cds_end": null,
"cds_length": 3081,
"cds_start": 2450,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "NM_001256214.2",
"gene_hgnc_id": 801,
"gene_symbol": "ATP1A3",
"hgvs_c": "c.2450C>T",
"hgvs_p": "p.Thr817Ile",
"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": "I",
"aa_end": null,
"aa_length": 1026,
"aa_ref": "T",
"aa_start": 817,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3628,
"cdna_start": 2644,
"cds_end": null,
"cds_length": 3081,
"cds_start": 2450,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "ENST00000545399.6",
"gene_hgnc_id": 801,
"gene_symbol": "ATP1A3",
"hgvs_c": "c.2450C>T",
"hgvs_p": "p.Thr817Ile",
"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": "I",
"aa_end": null,
"aa_length": 1024,
"aa_ref": "T",
"aa_start": 815,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3466,
"cdna_start": 2480,
"cds_end": null,
"cds_length": 3075,
"cds_start": 2444,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "NM_001256213.2",
"gene_hgnc_id": 801,
"gene_symbol": "ATP1A3",
"hgvs_c": "c.2444C>T",
"hgvs_p": "p.Thr815Ile",
"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": "I",
"aa_end": null,
"aa_length": 1024,
"aa_ref": "T",
"aa_start": 815,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3427,
"cdna_start": 2480,
"cds_end": null,
"cds_length": 3075,
"cds_start": 2444,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "ENST00000543770.5",
"gene_hgnc_id": 801,
"gene_symbol": "ATP1A3",
"hgvs_c": "c.2444C>T",
"hgvs_p": "p.Thr815Ile",
"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": "I",
"aa_end": null,
"aa_length": 996,
"aa_ref": "T",
"aa_start": 804,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3502,
"cdna_start": 2567,
"cds_end": null,
"cds_length": 2991,
"cds_start": 2411,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "ENST00000890880.1",
"gene_hgnc_id": 801,
"gene_symbol": "ATP1A3",
"hgvs_c": "c.2411C>T",
"hgvs_p": "p.Thr804Ile",
"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": "I",
"aa_end": null,
"aa_length": 994,
"aa_ref": "T",
"aa_start": 785,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3494,
"cdna_start": 2508,
"cds_end": null,
"cds_length": 2985,
"cds_start": 2354,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "ENST00000890884.1",
"gene_hgnc_id": 801,
"gene_symbol": "ATP1A3",
"hgvs_c": "c.2354C>T",
"hgvs_p": "p.Thr785Ile",
"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": "I",
"aa_end": null,
"aa_length": 984,
"aa_ref": "T",
"aa_start": 775,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3330,
"cdna_start": 2344,
"cds_end": null,
"cds_length": 2955,
"cds_start": 2324,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "ENST00000919566.1",
"gene_hgnc_id": 801,
"gene_symbol": "ATP1A3",
"hgvs_c": "c.2324C>T",
"hgvs_p": "p.Thr775Ile",
"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": "I",
"aa_end": null,
"aa_length": 983,
"aa_ref": "T",
"aa_start": 774,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3458,
"cdna_start": 2474,
"cds_end": null,
"cds_length": 2952,
"cds_start": 2321,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "ENST00000602133.5",
"gene_hgnc_id": 801,
"gene_symbol": "ATP1A3",
"hgvs_c": "c.2321C>T",
"hgvs_p": "p.Thr774Ile",
"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": "I",
"aa_end": null,
"aa_length": 945,
"aa_ref": "T",
"aa_start": 736,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3347,
"cdna_start": 2361,
"cds_end": null,
"cds_length": 2838,
"cds_start": 2207,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000890882.1",
"gene_hgnc_id": 801,
"gene_symbol": "ATP1A3",
"hgvs_c": "c.2207C>T",
"hgvs_p": "p.Thr736Ile",
"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": "I",
"aa_end": null,
"aa_length": 842,
"aa_ref": "T",
"aa_start": 633,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3034,
"cdna_start": 2050,
"cds_end": null,
"cds_length": 2529,
"cds_start": 1898,
"consequences": [
"missense_variant"
],
"exon_count": 19,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000948333.1",
"gene_hgnc_id": 801,
"gene_symbol": "ATP1A3",
"hgvs_c": "c.1898C>T",
"hgvs_p": "p.Thr633Ile",
"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": "I",
"aa_end": null,
"aa_length": 983,
"aa_ref": "T",
"aa_start": 774,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3410,
"cdna_start": 2424,
"cds_end": null,
"cds_length": 2952,
"cds_start": 2321,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "XM_047438862.1",
"gene_hgnc_id": 801,
"gene_symbol": "ATP1A3",
"hgvs_c": "c.2321C>T",
"hgvs_p": "p.Thr774Ile",
"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": 17,
"exon_rank_end": null,
"feature": "ENST00000441343.5",
"gene_hgnc_id": 801,
"gene_symbol": "ATP1A3",
"hgvs_c": "n.2411C>T",
"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": "rs606231438",
"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": null,
"phenotype_combined": null,
"phylop100way_prediction": "Pathogenic",
"phylop100way_score": 9.814,
"pos": 41970395,
"ref": "G",
"revel_prediction": "Pathogenic",
"revel_score": 0.981,
"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"
}
]
}