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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: 12-57038494-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=57038494&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 57038494,
"ref": "G",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000300119.8",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MYO1A",
"gene_hgnc_id": 7595,
"hgvs_c": "c.1678C>G",
"hgvs_p": "p.Pro560Ala",
"transcript": "NM_005379.4",
"protein_id": "NP_005370.1",
"transcript_support_level": null,
"aa_start": 560,
"aa_end": null,
"aa_length": 1043,
"cds_start": 1678,
"cds_end": null,
"cds_length": 3132,
"cdna_start": 1941,
"cdna_end": null,
"cdna_length": 3633,
"mane_select": "ENST00000300119.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "A",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MYO1A",
"gene_hgnc_id": 7595,
"hgvs_c": "c.1678C>G",
"hgvs_p": "p.Pro560Ala",
"transcript": "ENST00000300119.8",
"protein_id": "ENSP00000300119.3",
"transcript_support_level": 1,
"aa_start": 560,
"aa_end": null,
"aa_length": 1043,
"cds_start": 1678,
"cds_end": null,
"cds_length": 3132,
"cdna_start": 1941,
"cdna_end": null,
"cdna_length": 3633,
"mane_select": "NM_005379.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MYO1A",
"gene_hgnc_id": 7595,
"hgvs_c": "c.1678C>G",
"hgvs_p": "p.Pro560Ala",
"transcript": "ENST00000442789.6",
"protein_id": "ENSP00000393392.2",
"transcript_support_level": 1,
"aa_start": 560,
"aa_end": null,
"aa_length": 1043,
"cds_start": 1678,
"cds_end": null,
"cds_length": 3132,
"cdna_start": 1966,
"cdna_end": null,
"cdna_length": 3658,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MYO1A",
"gene_hgnc_id": 7595,
"hgvs_c": "c.1678C>G",
"hgvs_p": "p.Pro560Ala",
"transcript": "NM_001256041.2",
"protein_id": "NP_001242970.1",
"transcript_support_level": null,
"aa_start": 560,
"aa_end": null,
"aa_length": 1043,
"cds_start": 1678,
"cds_end": null,
"cds_length": 3132,
"cdna_start": 2399,
"cdna_end": null,
"cdna_length": 4091,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MYO1A",
"gene_hgnc_id": 7595,
"hgvs_c": "c.1678C>G",
"hgvs_p": "p.Pro560Ala",
"transcript": "XM_047428876.1",
"protein_id": "XP_047284832.1",
"transcript_support_level": null,
"aa_start": 560,
"aa_end": null,
"aa_length": 1043,
"cds_start": 1678,
"cds_end": null,
"cds_length": 3132,
"cdna_start": 1972,
"cdna_end": null,
"cdna_length": 3664,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MYO1A",
"gene_hgnc_id": 7595,
"hgvs_c": "c.1678C>G",
"hgvs_p": "p.Pro560Ala",
"transcript": "XM_011538373.3",
"protein_id": "XP_011536675.1",
"transcript_support_level": null,
"aa_start": 560,
"aa_end": null,
"aa_length": 866,
"cds_start": 1678,
"cds_end": null,
"cds_length": 2601,
"cdna_start": 1941,
"cdna_end": null,
"cdna_length": 2980,
"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": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MYO1A",
"gene_hgnc_id": 7595,
"hgvs_c": "n.575C>G",
"hgvs_p": null,
"transcript": "ENST00000476795.1",
"protein_id": null,
"transcript_support_level": 5,
"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": 631,
"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": 13,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MYO1A",
"gene_hgnc_id": 7595,
"hgvs_c": "n.1192C>G",
"hgvs_p": null,
"transcript": "ENST00000554234.5",
"protein_id": "ENSP00000451033.1",
"transcript_support_level": 5,
"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": 3099,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "MYO1A",
"gene_hgnc_id": 7595,
"dbsnp": "rs140586750",
"frequency_reference_population": 0.000030357474,
"hom_count_reference_population": 0,
"allele_count_reference_population": 49,
"gnomad_exomes_af": 0.000030098,
"gnomad_genomes_af": 0.0000328498,
"gnomad_exomes_ac": 44,
"gnomad_genomes_ac": 5,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8439311385154724,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.55,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.1683,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.09,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 9.992,
"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": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PP3_Moderate,BS2",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PP3_Moderate",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "ENST00000300119.8",
"gene_symbol": "MYO1A",
"hgnc_id": 7595,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.1678C>G",
"hgvs_p": "p.Pro560Ala"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:2",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}