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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: 9-108934555-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=108934555&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "9",
"pos": 108934555,
"ref": "G",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_017832.4",
"consequences": [
{
"aa_ref": "W",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABITRAM",
"gene_hgnc_id": 1364,
"hgvs_c": "c.69G>C",
"hgvs_p": "p.Trp23Cys",
"transcript": "NM_017832.4",
"protein_id": "NP_060302.1",
"transcript_support_level": null,
"aa_start": 23,
"aa_end": null,
"aa_length": 181,
"cds_start": 69,
"cds_end": null,
"cds_length": 546,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000322940.11",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_017832.4"
},
{
"aa_ref": "W",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABITRAM",
"gene_hgnc_id": 1364,
"hgvs_c": "c.69G>C",
"hgvs_p": "p.Trp23Cys",
"transcript": "ENST00000322940.11",
"protein_id": "ENSP00000363753.3",
"transcript_support_level": 1,
"aa_start": 23,
"aa_end": null,
"aa_length": 181,
"cds_start": 69,
"cds_end": null,
"cds_length": 546,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_017832.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000322940.11"
},
{
"aa_ref": "W",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABITRAM",
"gene_hgnc_id": 1364,
"hgvs_c": "c.69G>C",
"hgvs_p": "p.Trp23Cys",
"transcript": "ENST00000964591.1",
"protein_id": "ENSP00000634650.1",
"transcript_support_level": null,
"aa_start": 23,
"aa_end": null,
"aa_length": 181,
"cds_start": 69,
"cds_end": null,
"cds_length": 546,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000964591.1"
},
{
"aa_ref": "W",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABITRAM",
"gene_hgnc_id": 1364,
"hgvs_c": "c.69G>C",
"hgvs_p": "p.Trp23Cys",
"transcript": "ENST00000919245.1",
"protein_id": "ENSP00000589304.1",
"transcript_support_level": null,
"aa_start": 23,
"aa_end": null,
"aa_length": 174,
"cds_start": 69,
"cds_end": null,
"cds_length": 525,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000919245.1"
},
{
"aa_ref": "W",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABITRAM",
"gene_hgnc_id": 1364,
"hgvs_c": "c.69G>C",
"hgvs_p": "p.Trp23Cys",
"transcript": "ENST00000899979.1",
"protein_id": "ENSP00000570038.1",
"transcript_support_level": null,
"aa_start": 23,
"aa_end": null,
"aa_length": 156,
"cds_start": 69,
"cds_end": null,
"cds_length": 471,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000899979.1"
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABITRAM",
"gene_hgnc_id": 1364,
"hgvs_c": "c.16G>C",
"hgvs_p": "p.Val6Leu",
"transcript": "ENST00000445175.1",
"protein_id": "ENSP00000398018.1",
"transcript_support_level": 3,
"aa_start": 6,
"aa_end": null,
"aa_length": 128,
"cds_start": 16,
"cds_end": null,
"cds_length": 389,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000445175.1"
},
{
"aa_ref": "W",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABITRAM",
"gene_hgnc_id": 1364,
"hgvs_c": "c.69G>C",
"hgvs_p": "p.Trp23Cys",
"transcript": "NM_001410990.1",
"protein_id": "NP_001397919.1",
"transcript_support_level": null,
"aa_start": 23,
"aa_end": null,
"aa_length": 115,
"cds_start": 69,
"cds_end": null,
"cds_length": 348,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001410990.1"
},
{
"aa_ref": "W",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABITRAM",
"gene_hgnc_id": 1364,
"hgvs_c": "c.69G>C",
"hgvs_p": "p.Trp23Cys",
"transcript": "ENST00000374624.7",
"protein_id": "ENSP00000363754.3",
"transcript_support_level": 3,
"aa_start": 23,
"aa_end": null,
"aa_length": 115,
"cds_start": 69,
"cds_end": null,
"cds_length": 348,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000374624.7"
},
{
"aa_ref": "W",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABITRAM",
"gene_hgnc_id": 1364,
"hgvs_c": "c.69G>C",
"hgvs_p": "p.Trp23Cys",
"transcript": "ENST00000964592.1",
"protein_id": "ENSP00000634651.1",
"transcript_support_level": null,
"aa_start": 23,
"aa_end": null,
"aa_length": 112,
"cds_start": 69,
"cds_end": null,
"cds_length": 339,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000964592.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABITRAM",
"gene_hgnc_id": 1364,
"hgvs_c": "n.113G>C",
"hgvs_p": null,
"transcript": "ENST00000466200.1",
"protein_id": null,
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000466200.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 38,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ELP1",
"gene_hgnc_id": 5959,
"hgvs_c": "c.-444C>G",
"hgvs_p": null,
"transcript": "ENST00000861104.1",
"protein_id": "ENSP00000531163.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1332,
"cds_start": null,
"cds_end": null,
"cds_length": 3999,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000861104.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 37,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ELP1",
"gene_hgnc_id": 5959,
"hgvs_c": "c.-944C>G",
"hgvs_p": null,
"transcript": "ENST00000674948.1",
"protein_id": "ENSP00000501602.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1218,
"cds_start": null,
"cds_end": null,
"cds_length": 3657,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000674948.1"
}
],
"gene_symbol": "ABITRAM",
"gene_hgnc_id": 1364,
"dbsnp": "rs370627190",
"frequency_reference_population": 0.0000027533722,
"hom_count_reference_population": 0,
"allele_count_reference_population": 4,
"gnomad_exomes_af": 0.00000275337,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 4,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.4410831928253174,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.763,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9585,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": 0.33,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 5.688,
"phylop100way_prediction": "Uncertain_significance",
"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": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "NM_017832.4",
"gene_symbol": "ABITRAM",
"hgnc_id": 1364,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.69G>C",
"hgvs_p": "p.Trp23Cys"
},
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000861104.1",
"gene_symbol": "ELP1",
"hgnc_id": 5959,
"effects": [
"upstream_gene_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.-444C>G",
"hgvs_p": null
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}