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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: 19-1784856-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=1784856&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "ATP8B3",
"hgnc_id": 13535,
"hgvs_c": "c.3623G>A",
"hgvs_p": "p.Arg1208Gln",
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": 2,
"transcript": "NM_138813.4",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_score": 2,
"allele_count_reference_population": 11,
"alphamissense_prediction": null,
"alphamissense_score": 0.114,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.27,
"chr": "19",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Uncertain_significance",
"computational_score_selected": 0.5638437271118164,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 1300,
"aa_ref": "R",
"aa_start": 1208,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5095,
"cdna_start": 3862,
"cds_end": null,
"cds_length": 3903,
"cds_start": 3623,
"consequences": [
"missense_variant"
],
"exon_count": 29,
"exon_rank": 28,
"exon_rank_end": null,
"feature": "NM_138813.4",
"gene_hgnc_id": 13535,
"gene_symbol": "ATP8B3",
"hgvs_c": "c.3623G>A",
"hgvs_p": "p.Arg1208Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000310127.10",
"protein_coding": true,
"protein_id": "NP_620168.1",
"strand": false,
"transcript": "NM_138813.4",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 1300,
"aa_ref": "R",
"aa_start": 1208,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 5095,
"cdna_start": 3862,
"cds_end": null,
"cds_length": 3903,
"cds_start": 3623,
"consequences": [
"missense_variant"
],
"exon_count": 29,
"exon_rank": 28,
"exon_rank_end": null,
"feature": "ENST00000310127.10",
"gene_hgnc_id": 13535,
"gene_symbol": "ATP8B3",
"hgvs_c": "c.3623G>A",
"hgvs_p": "p.Arg1208Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_138813.4",
"protein_coding": true,
"protein_id": "ENSP00000311336.6",
"strand": false,
"transcript": "ENST00000310127.10",
"transcript_support_level": 1
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 1263,
"aa_ref": "R",
"aa_start": 1171,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4014,
"cdna_start": 3734,
"cds_end": null,
"cds_length": 3792,
"cds_start": 3512,
"consequences": [
"missense_variant"
],
"exon_count": 29,
"exon_rank": 28,
"exon_rank_end": null,
"feature": "ENST00000525591.5",
"gene_hgnc_id": 13535,
"gene_symbol": "ATP8B3",
"hgvs_c": "c.3512G>A",
"hgvs_p": "p.Arg1171Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000437115.1",
"strand": false,
"transcript": "ENST00000525591.5",
"transcript_support_level": 1
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 1263,
"aa_ref": "R",
"aa_start": 1171,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5043,
"cdna_start": 3810,
"cds_end": null,
"cds_length": 3792,
"cds_start": 3512,
"consequences": [
"missense_variant"
],
"exon_count": 29,
"exon_rank": 28,
"exon_rank_end": null,
"feature": "NM_001178002.3",
"gene_hgnc_id": 13535,
"gene_symbol": "ATP8B3",
"hgvs_c": "c.3512G>A",
"hgvs_p": "p.Arg1171Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001171473.1",
"strand": false,
"transcript": "NM_001178002.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 5237,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 29,
"exon_rank": 28,
"exon_rank_end": null,
"feature": "ENST00000531925.5",
"gene_hgnc_id": 13535,
"gene_symbol": "ATP8B3",
"hgvs_c": "n.*3506G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000444334.1",
"strand": false,
"transcript": "ENST00000531925.5",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 5239,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 29,
"exon_rank": 28,
"exon_rank_end": null,
"feature": "NR_047593.3",
"gene_hgnc_id": 13535,
"gene_symbol": "ATP8B3",
"hgvs_c": "n.4006G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "NR_047593.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 5237,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 29,
"exon_rank": 28,
"exon_rank_end": null,
"feature": "ENST00000531925.5",
"gene_hgnc_id": 13535,
"gene_symbol": "ATP8B3",
"hgvs_c": "n.*3506G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000444334.1",
"strand": false,
"transcript": "ENST00000531925.5",
"transcript_support_level": 2
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs781549083",
"effect": "missense_variant",
"frequency_reference_population": 0.000007541385,
"gene_hgnc_id": 13535,
"gene_symbol": "ATP8B3",
"gnomad_exomes_ac": 11,
"gnomad_exomes_af": 0.00000754139,
"gnomad_exomes_homalt": 0,
"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": "Uncertain significance",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Benign",
"phylop100way_score": 0.999,
"pos": 1784856,
"ref": "C",
"revel_prediction": "Uncertain_significance",
"revel_score": 0.394,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.019999999552965164,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.02,
"transcript": "NM_138813.4"
}
]
}