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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: 5-141580754-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=141580754&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 141580754,
"ref": "G",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000647433.1",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DIAPH1",
"gene_hgnc_id": 2876,
"hgvs_c": "c.814C>G",
"hgvs_p": "p.Pro272Ala",
"transcript": "NM_005219.5",
"protein_id": "NP_005210.3",
"transcript_support_level": null,
"aa_start": 272,
"aa_end": null,
"aa_length": 1272,
"cds_start": 814,
"cds_end": null,
"cds_length": 3819,
"cdna_start": 900,
"cdna_end": null,
"cdna_length": 5735,
"mane_select": "ENST00000389054.8",
"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": 8,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DIAPH1",
"gene_hgnc_id": 2876,
"hgvs_c": "c.814C>G",
"hgvs_p": "p.Pro272Ala",
"transcript": "ENST00000389054.8",
"protein_id": "ENSP00000373706.4",
"transcript_support_level": 5,
"aa_start": 272,
"aa_end": null,
"aa_length": 1272,
"cds_start": 814,
"cds_end": null,
"cds_length": 3819,
"cdna_start": 900,
"cdna_end": null,
"cdna_length": 5735,
"mane_select": "NM_005219.5",
"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": 7,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DIAPH1",
"gene_hgnc_id": 2876,
"hgvs_c": "c.787C>G",
"hgvs_p": "p.Pro263Ala",
"transcript": "ENST00000518047.5",
"protein_id": "ENSP00000428268.2",
"transcript_support_level": 5,
"aa_start": 263,
"aa_end": null,
"aa_length": 1263,
"cds_start": 787,
"cds_end": null,
"cds_length": 3792,
"cdna_start": 787,
"cdna_end": null,
"cdna_length": 4668,
"mane_select": null,
"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": 8,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DIAPH1",
"gene_hgnc_id": 2876,
"hgvs_c": "c.814C>G",
"hgvs_p": "p.Pro272Ala",
"transcript": "ENST00000647433.1",
"protein_id": "ENSP00000494675.1",
"transcript_support_level": null,
"aa_start": 272,
"aa_end": null,
"aa_length": 1250,
"cds_start": 814,
"cds_end": null,
"cds_length": 3753,
"cdna_start": 955,
"cdna_end": null,
"cdna_length": 5843,
"mane_select": null,
"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": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DIAPH1",
"gene_hgnc_id": 2876,
"hgvs_c": "n.*41C>G",
"hgvs_p": null,
"transcript": "ENST00000523100.5",
"protein_id": "ENSP00000428208.1",
"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": 1180,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DIAPH1",
"gene_hgnc_id": 2876,
"hgvs_c": "n.*41C>G",
"hgvs_p": null,
"transcript": "ENST00000523100.5",
"protein_id": "ENSP00000428208.1",
"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": 1180,
"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": 7,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DIAPH1",
"gene_hgnc_id": 2876,
"hgvs_c": "c.787C>G",
"hgvs_p": "p.Pro263Ala",
"transcript": "NM_001079812.3",
"protein_id": "NP_001073280.1",
"transcript_support_level": null,
"aa_start": 263,
"aa_end": null,
"aa_length": 1263,
"cds_start": 787,
"cds_end": null,
"cds_length": 3792,
"cdna_start": 873,
"cdna_end": null,
"cdna_length": 5708,
"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": 8,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DIAPH1",
"gene_hgnc_id": 2876,
"hgvs_c": "c.814C>G",
"hgvs_p": "p.Pro272Ala",
"transcript": "NM_001314007.2",
"protein_id": "NP_001300936.1",
"transcript_support_level": null,
"aa_start": 272,
"aa_end": null,
"aa_length": 1250,
"cds_start": 814,
"cds_end": null,
"cds_length": 3753,
"cdna_start": 900,
"cdna_end": null,
"cdna_length": 5788,
"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": 7,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DIAPH1",
"gene_hgnc_id": 2876,
"hgvs_c": "c.778C>G",
"hgvs_p": "p.Pro260Ala",
"transcript": "XM_047416884.1",
"protein_id": "XP_047272840.1",
"transcript_support_level": null,
"aa_start": 260,
"aa_end": null,
"aa_length": 1260,
"cds_start": 778,
"cds_end": null,
"cds_length": 3783,
"cdna_start": 1546,
"cdna_end": null,
"cdna_length": 6381,
"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": 8,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DIAPH1",
"gene_hgnc_id": 2876,
"hgvs_c": "c.748C>G",
"hgvs_p": "p.Pro250Ala",
"transcript": "XM_047416885.1",
"protein_id": "XP_047272841.1",
"transcript_support_level": null,
"aa_start": 250,
"aa_end": null,
"aa_length": 1250,
"cds_start": 748,
"cds_end": null,
"cds_length": 3753,
"cdna_start": 1000,
"cdna_end": null,
"cdna_length": 5835,
"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": 7,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DIAPH1",
"gene_hgnc_id": 2876,
"hgvs_c": "n.*41C>G",
"hgvs_p": null,
"transcript": "ENST00000647330.1",
"protein_id": "ENSP00000494308.1",
"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": 1795,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DIAPH1",
"gene_hgnc_id": 2876,
"hgvs_c": "n.*41C>G",
"hgvs_p": null,
"transcript": "ENST00000647330.1",
"protein_id": "ENSP00000494308.1",
"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": 1795,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "DIAPH1",
"gene_hgnc_id": 2876,
"dbsnp": "rs778493344",
"frequency_reference_population": 0.0000020523541,
"hom_count_reference_population": 0,
"allele_count_reference_population": 3,
"gnomad_exomes_af": 0.00000205235,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 3,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.5545147061347961,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.09000000357627869,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.557,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.1317,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.07,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 3.789,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.09,
"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": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000647433.1",
"gene_symbol": "DIAPH1",
"hgnc_id": 2876,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.814C>G",
"hgvs_p": "p.Pro272Ala"
}
],
"clinvar_disease": "Autosomal dominant nonsyndromic hearing loss 1,Progressive microcephaly-seizures-cortical blindness-developmental delay syndrome,not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:2",
"phenotype_combined": "not specified|Autosomal dominant nonsyndromic hearing loss 1;Progressive microcephaly-seizures-cortical blindness-developmental delay syndrome",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}