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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: 11-63636274-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=11&pos=63636274&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "11",
"pos": 63636274,
"ref": "G",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_015459.5",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATL3",
"gene_hgnc_id": 24526,
"hgvs_c": "c.911C>G",
"hgvs_p": "p.Ser304Cys",
"transcript": "NM_015459.5",
"protein_id": "NP_056274.3",
"transcript_support_level": null,
"aa_start": 304,
"aa_end": null,
"aa_length": 541,
"cds_start": 911,
"cds_end": null,
"cds_length": 1626,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000398868.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_015459.5"
},
{
"aa_ref": "S",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATL3",
"gene_hgnc_id": 24526,
"hgvs_c": "c.911C>G",
"hgvs_p": "p.Ser304Cys",
"transcript": "ENST00000398868.8",
"protein_id": "ENSP00000381844.3",
"transcript_support_level": 1,
"aa_start": 304,
"aa_end": null,
"aa_length": 541,
"cds_start": 911,
"cds_end": null,
"cds_length": 1626,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_015459.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000398868.8"
},
{
"aa_ref": "S",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATL3",
"gene_hgnc_id": 24526,
"hgvs_c": "c.908C>G",
"hgvs_p": "p.Ser303Cys",
"transcript": "ENST00000955365.1",
"protein_id": "ENSP00000625424.1",
"transcript_support_level": null,
"aa_start": 303,
"aa_end": null,
"aa_length": 540,
"cds_start": 908,
"cds_end": null,
"cds_length": 1623,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000955365.1"
},
{
"aa_ref": "S",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATL3",
"gene_hgnc_id": 24526,
"hgvs_c": "c.860C>G",
"hgvs_p": "p.Ser287Cys",
"transcript": "NM_001440716.1",
"protein_id": "NP_001427645.1",
"transcript_support_level": null,
"aa_start": 287,
"aa_end": null,
"aa_length": 524,
"cds_start": 860,
"cds_end": null,
"cds_length": 1575,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001440716.1"
},
{
"aa_ref": "S",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATL3",
"gene_hgnc_id": 24526,
"hgvs_c": "c.857C>G",
"hgvs_p": "p.Ser286Cys",
"transcript": "NM_001290048.2",
"protein_id": "NP_001276977.1",
"transcript_support_level": null,
"aa_start": 286,
"aa_end": null,
"aa_length": 523,
"cds_start": 857,
"cds_end": null,
"cds_length": 1572,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001290048.2"
},
{
"aa_ref": "S",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATL3",
"gene_hgnc_id": 24526,
"hgvs_c": "c.857C>G",
"hgvs_p": "p.Ser286Cys",
"transcript": "ENST00000538786.1",
"protein_id": "ENSP00000437593.1",
"transcript_support_level": 2,
"aa_start": 286,
"aa_end": null,
"aa_length": 523,
"cds_start": 857,
"cds_end": null,
"cds_length": 1572,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000538786.1"
},
{
"aa_ref": "S",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATL3",
"gene_hgnc_id": 24526,
"hgvs_c": "c.854C>G",
"hgvs_p": "p.Ser285Cys",
"transcript": "NM_001440717.1",
"protein_id": "NP_001427646.1",
"transcript_support_level": null,
"aa_start": 285,
"aa_end": null,
"aa_length": 522,
"cds_start": 854,
"cds_end": null,
"cds_length": 1569,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001440717.1"
},
{
"aa_ref": "S",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATL3",
"gene_hgnc_id": 24526,
"hgvs_c": "c.911C>G",
"hgvs_p": "p.Ser304Cys",
"transcript": "NM_001440718.1",
"protein_id": "NP_001427647.1",
"transcript_support_level": null,
"aa_start": 304,
"aa_end": null,
"aa_length": 517,
"cds_start": 911,
"cds_end": null,
"cds_length": 1554,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001440718.1"
},
{
"aa_ref": "S",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATL3",
"gene_hgnc_id": 24526,
"hgvs_c": "c.806C>G",
"hgvs_p": "p.Ser269Cys",
"transcript": "NM_001440719.1",
"protein_id": "NP_001427648.1",
"transcript_support_level": null,
"aa_start": 269,
"aa_end": null,
"aa_length": 506,
"cds_start": 806,
"cds_end": null,
"cds_length": 1521,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001440719.1"
},
{
"aa_ref": "S",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATL3",
"gene_hgnc_id": 24526,
"hgvs_c": "c.800C>G",
"hgvs_p": "p.Ser267Cys",
"transcript": "NM_001440720.1",
"protein_id": "NP_001427649.1",
"transcript_support_level": null,
"aa_start": 267,
"aa_end": null,
"aa_length": 504,
"cds_start": 800,
"cds_end": null,
"cds_length": 1515,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001440720.1"
},
{
"aa_ref": "S",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATL3",
"gene_hgnc_id": 24526,
"hgvs_c": "c.755C>G",
"hgvs_p": "p.Ser252Cys",
"transcript": "NM_001440721.1",
"protein_id": "NP_001427650.1",
"transcript_support_level": null,
"aa_start": 252,
"aa_end": null,
"aa_length": 489,
"cds_start": 755,
"cds_end": null,
"cds_length": 1470,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001440721.1"
},
{
"aa_ref": "S",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATL3",
"gene_hgnc_id": 24526,
"hgvs_c": "c.698C>G",
"hgvs_p": "p.Ser233Cys",
"transcript": "NM_001440722.1",
"protein_id": "NP_001427651.1",
"transcript_support_level": null,
"aa_start": 233,
"aa_end": null,
"aa_length": 470,
"cds_start": 698,
"cds_end": null,
"cds_length": 1413,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001440722.1"
},
{
"aa_ref": "S",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATL3",
"gene_hgnc_id": 24526,
"hgvs_c": "c.1067C>G",
"hgvs_p": "p.Ser356Cys",
"transcript": "XM_047426725.1",
"protein_id": "XP_047282681.1",
"transcript_support_level": null,
"aa_start": 356,
"aa_end": null,
"aa_length": 593,
"cds_start": 1067,
"cds_end": null,
"cds_length": 1782,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047426725.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "LNCROPM",
"gene_hgnc_id": 58146,
"hgvs_c": "n.121-1217G>C",
"hgvs_p": null,
"transcript": "ENST00000540307.2",
"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": "ENST00000540307.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "LNCROPM",
"gene_hgnc_id": 58146,
"hgvs_c": "n.106-1217G>C",
"hgvs_p": null,
"transcript": "NR_199012.1",
"protein_id": null,
"transcript_support_level": null,
"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": "NR_199012.1"
}
],
"gene_symbol": "ATL3",
"gene_hgnc_id": 24526,
"dbsnp": "rs757344746",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.170680969953537,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.243,
"revel_prediction": "Benign",
"alphamissense_score": 0.0894,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.33,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.76,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.02,
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_015459.5",
"gene_symbol": "ATL3",
"hgnc_id": 24526,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.911C>G",
"hgvs_p": "p.Ser304Cys"
},
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000540307.2",
"gene_symbol": "LNCROPM",
"hgnc_id": 58146,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.121-1217G>C",
"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
}