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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: 1-109921971-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=109921971&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 109921971,
"ref": "G",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_000757.6",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSF1",
"gene_hgnc_id": 2432,
"hgvs_c": "c.521G>T",
"hgvs_p": "p.Ser174Ile",
"transcript": "NM_000757.6",
"protein_id": "NP_000748.4",
"transcript_support_level": null,
"aa_start": 174,
"aa_end": null,
"aa_length": 554,
"cds_start": 521,
"cds_end": null,
"cds_length": 1665,
"cdna_start": 696,
"cdna_end": null,
"cdna_length": 3994,
"mane_select": "ENST00000329608.11",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "I",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSF1",
"gene_hgnc_id": 2432,
"hgvs_c": "c.521G>T",
"hgvs_p": "p.Ser174Ile",
"transcript": "ENST00000329608.11",
"protein_id": "ENSP00000327513.6",
"transcript_support_level": 1,
"aa_start": 174,
"aa_end": null,
"aa_length": 554,
"cds_start": 521,
"cds_end": null,
"cds_length": 1665,
"cdna_start": 696,
"cdna_end": null,
"cdna_length": 3994,
"mane_select": "NM_000757.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSF1",
"gene_hgnc_id": 2432,
"hgvs_c": "c.521G>T",
"hgvs_p": "p.Ser174Ile",
"transcript": "ENST00000369802.7",
"protein_id": "ENSP00000358817.3",
"transcript_support_level": 1,
"aa_start": 174,
"aa_end": null,
"aa_length": 554,
"cds_start": 521,
"cds_end": null,
"cds_length": 1665,
"cdna_start": 646,
"cdna_end": null,
"cdna_length": 2484,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSF1",
"gene_hgnc_id": 2432,
"hgvs_c": "c.521G>T",
"hgvs_p": "p.Ser174Ile",
"transcript": "ENST00000369801.1",
"protein_id": "ENSP00000358816.1",
"transcript_support_level": 1,
"aa_start": 174,
"aa_end": null,
"aa_length": 438,
"cds_start": 521,
"cds_end": null,
"cds_length": 1317,
"cdna_start": 559,
"cdna_end": null,
"cdna_length": 1364,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSF1",
"gene_hgnc_id": 2432,
"hgvs_c": "c.521G>T",
"hgvs_p": "p.Ser174Ile",
"transcript": "NM_172212.3",
"protein_id": "NP_757351.2",
"transcript_support_level": null,
"aa_start": 174,
"aa_end": null,
"aa_length": 554,
"cds_start": 521,
"cds_end": null,
"cds_length": 1665,
"cdna_start": 696,
"cdna_end": null,
"cdna_length": 2535,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSF1",
"gene_hgnc_id": 2432,
"hgvs_c": "c.521G>T",
"hgvs_p": "p.Ser174Ile",
"transcript": "NM_172210.3",
"protein_id": "NP_757349.2",
"transcript_support_level": null,
"aa_start": 174,
"aa_end": null,
"aa_length": 438,
"cds_start": 521,
"cds_end": null,
"cds_length": 1317,
"cdna_start": 696,
"cdna_end": null,
"cdna_length": 1505,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSF1",
"gene_hgnc_id": 2432,
"hgvs_c": "c.398G>T",
"hgvs_p": "p.Ser133Ile",
"transcript": "ENST00000488198.5",
"protein_id": "ENSP00000433837.1",
"transcript_support_level": 3,
"aa_start": 133,
"aa_end": null,
"aa_length": 284,
"cds_start": 398,
"cds_end": null,
"cds_length": 855,
"cdna_start": 552,
"cdna_end": null,
"cdna_length": 1009,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSF1",
"gene_hgnc_id": 2432,
"hgvs_c": "c.521G>T",
"hgvs_p": "p.Ser174Ile",
"transcript": "NM_172211.4",
"protein_id": "NP_757350.2",
"transcript_support_level": null,
"aa_start": 174,
"aa_end": null,
"aa_length": 256,
"cds_start": 521,
"cds_end": null,
"cds_length": 771,
"cdna_start": 696,
"cdna_end": null,
"cdna_length": 3100,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSF1",
"gene_hgnc_id": 2432,
"hgvs_c": "c.521G>T",
"hgvs_p": "p.Ser174Ile",
"transcript": "ENST00000420111.6",
"protein_id": "ENSP00000407317.2",
"transcript_support_level": 5,
"aa_start": 174,
"aa_end": null,
"aa_length": 256,
"cds_start": 521,
"cds_end": null,
"cds_length": 771,
"cdna_start": 637,
"cdna_end": null,
"cdna_length": 1083,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSF1",
"gene_hgnc_id": 2432,
"hgvs_c": "c.398G>T",
"hgvs_p": "p.Ser133Ile",
"transcript": "XM_017000369.1",
"protein_id": "XP_016855858.1",
"transcript_support_level": null,
"aa_start": 133,
"aa_end": null,
"aa_length": 513,
"cds_start": 398,
"cds_end": null,
"cds_length": 1542,
"cdna_start": 609,
"cdna_end": null,
"cdna_length": 3907,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSF1",
"gene_hgnc_id": 2432,
"hgvs_c": "c.521G>T",
"hgvs_p": "p.Ser174Ile",
"transcript": "XM_047446752.1",
"protein_id": "XP_047302708.1",
"transcript_support_level": null,
"aa_start": 174,
"aa_end": null,
"aa_length": 256,
"cds_start": 521,
"cds_end": null,
"cds_length": 771,
"cdna_start": 696,
"cdna_end": null,
"cdna_length": 1641,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSF1",
"gene_hgnc_id": 2432,
"hgvs_c": "n.336G>T",
"hgvs_p": null,
"transcript": "ENST00000526001.1",
"protein_id": null,
"transcript_support_level": 4,
"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": 573,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSF1",
"gene_hgnc_id": 2432,
"hgvs_c": "c.*91G>T",
"hgvs_p": null,
"transcript": "ENST00000527192.5",
"protein_id": "ENSP00000434527.1",
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": 149,
"cds_start": -4,
"cds_end": null,
"cds_length": 451,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 577,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSF1",
"gene_hgnc_id": 2432,
"hgvs_c": "c.*58G>T",
"hgvs_p": null,
"transcript": "ENST00000525659.5",
"protein_id": "ENSP00000431547.1",
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": 112,
"cds_start": -4,
"cds_end": null,
"cds_length": 340,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 551,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "CSF1",
"gene_hgnc_id": 2432,
"dbsnp": "rs200625266",
"frequency_reference_population": 0.000057922054,
"hom_count_reference_population": 0,
"allele_count_reference_population": 93,
"gnomad_exomes_af": 0.0000481686,
"gnomad_genomes_af": 0.00015094,
"gnomad_exomes_ac": 70,
"gnomad_genomes_ac": 23,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.22401344776153564,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.063,
"revel_prediction": "Benign",
"alphamissense_score": 0.1522,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.58,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.297,
"phylop100way_prediction": "Benign",
"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": -6,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate,BS2",
"acmg_by_gene": [
{
"score": -6,
"benign_score": 6,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "NM_000757.6",
"gene_symbol": "CSF1",
"hgnc_id": 2432,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.521G>T",
"hgvs_p": "p.Ser174Ile"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}