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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: X-70454284-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=70454284&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 70454284,
"ref": "C",
"alt": "A",
"effect": "stop_gained",
"transcript": "ENST00000374360.8",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DLG3",
"gene_hgnc_id": 2902,
"hgvs_c": "c.1373C>A",
"hgvs_p": "p.Ser458*",
"transcript": "NM_021120.4",
"protein_id": "NP_066943.2",
"transcript_support_level": null,
"aa_start": 458,
"aa_end": null,
"aa_length": 817,
"cds_start": 1373,
"cds_end": null,
"cds_length": 2454,
"cdna_start": 1740,
"cdna_end": null,
"cdna_length": 6042,
"mane_select": "ENST00000374360.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DLG3",
"gene_hgnc_id": 2902,
"hgvs_c": "c.1373C>A",
"hgvs_p": "p.Ser458*",
"transcript": "ENST00000374360.8",
"protein_id": "ENSP00000363480.3",
"transcript_support_level": 1,
"aa_start": 458,
"aa_end": null,
"aa_length": 817,
"cds_start": 1373,
"cds_end": null,
"cds_length": 2454,
"cdna_start": 1740,
"cdna_end": null,
"cdna_length": 6042,
"mane_select": "NM_021120.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DLG3",
"gene_hgnc_id": 2902,
"hgvs_c": "c.362C>A",
"hgvs_p": "p.Ser121*",
"transcript": "ENST00000374355.8",
"protein_id": "ENSP00000363475.3",
"transcript_support_level": 1,
"aa_start": 121,
"aa_end": null,
"aa_length": 512,
"cds_start": 362,
"cds_end": null,
"cds_length": 1539,
"cdna_start": 692,
"cdna_end": null,
"cdna_length": 5090,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DLG3",
"gene_hgnc_id": 2902,
"hgvs_c": "c.1427C>A",
"hgvs_p": "p.Ser476*",
"transcript": "ENST00000194900.8",
"protein_id": "ENSP00000194900.4",
"transcript_support_level": 5,
"aa_start": 476,
"aa_end": null,
"aa_length": 849,
"cds_start": 1427,
"cds_end": null,
"cds_length": 2550,
"cdna_start": 1768,
"cdna_end": null,
"cdna_length": 6112,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DLG3",
"gene_hgnc_id": 2902,
"hgvs_c": "c.362C>A",
"hgvs_p": "p.Ser121*",
"transcript": "NM_020730.3",
"protein_id": "NP_065781.1",
"transcript_support_level": null,
"aa_start": 121,
"aa_end": null,
"aa_length": 512,
"cds_start": 362,
"cds_end": null,
"cds_length": 1539,
"cdna_start": 692,
"cdna_end": null,
"cdna_length": 5090,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DLG3",
"gene_hgnc_id": 2902,
"hgvs_c": "c.1373C>A",
"hgvs_p": "p.Ser458*",
"transcript": "XM_006724625.3",
"protein_id": "XP_006724688.1",
"transcript_support_level": null,
"aa_start": 458,
"aa_end": null,
"aa_length": 849,
"cds_start": 1373,
"cds_end": null,
"cds_length": 2550,
"cdna_start": 1740,
"cdna_end": null,
"cdna_length": 6138,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DLG3",
"gene_hgnc_id": 2902,
"hgvs_c": "c.1373C>A",
"hgvs_p": "p.Ser458*",
"transcript": "XM_011530883.2",
"protein_id": "XP_011529185.1",
"transcript_support_level": null,
"aa_start": 458,
"aa_end": null,
"aa_length": 835,
"cds_start": 1373,
"cds_end": null,
"cds_length": 2508,
"cdna_start": 1740,
"cdna_end": null,
"cdna_length": 6096,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DLG3",
"gene_hgnc_id": 2902,
"hgvs_c": "c.1373C>A",
"hgvs_p": "p.Ser458*",
"transcript": "XM_006724626.3",
"protein_id": "XP_006724689.1",
"transcript_support_level": null,
"aa_start": 458,
"aa_end": null,
"aa_length": 831,
"cds_start": 1373,
"cds_end": null,
"cds_length": 2496,
"cdna_start": 1740,
"cdna_end": null,
"cdna_length": 6084,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DLG3",
"gene_hgnc_id": 2902,
"hgvs_c": "c.362C>A",
"hgvs_p": "p.Ser121*",
"transcript": "XM_017029322.3",
"protein_id": "XP_016884811.1",
"transcript_support_level": null,
"aa_start": 121,
"aa_end": null,
"aa_length": 498,
"cds_start": 362,
"cds_end": null,
"cds_length": 1497,
"cdna_start": 692,
"cdna_end": null,
"cdna_length": 5048,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DLG3",
"gene_hgnc_id": 2902,
"hgvs_c": "c.362C>A",
"hgvs_p": "p.Ser121*",
"transcript": "XM_017029323.3",
"protein_id": "XP_016884812.1",
"transcript_support_level": null,
"aa_start": 121,
"aa_end": null,
"aa_length": 494,
"cds_start": 362,
"cds_end": null,
"cds_length": 1485,
"cdna_start": 692,
"cdna_end": null,
"cdna_length": 5036,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DLG3",
"gene_hgnc_id": 2902,
"hgvs_c": "c.362C>A",
"hgvs_p": "p.Ser121*",
"transcript": "XM_017029324.3",
"protein_id": "XP_016884813.1",
"transcript_support_level": null,
"aa_start": 121,
"aa_end": null,
"aa_length": 480,
"cds_start": 362,
"cds_end": null,
"cds_length": 1443,
"cdna_start": 692,
"cdna_end": null,
"cdna_length": 4994,
"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": 8,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DLG3",
"gene_hgnc_id": 2902,
"hgvs_c": "n.1772C>A",
"hgvs_p": null,
"transcript": "ENST00000463252.5",
"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": 4626,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DLG3",
"gene_hgnc_id": 2902,
"hgvs_c": "c.-77C>A",
"hgvs_p": null,
"transcript": "XM_005262248.5",
"protein_id": "XP_005262305.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 366,
"cds_start": -4,
"cds_end": null,
"cds_length": 1101,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4871,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "DLG3-AS1",
"gene_hgnc_id": 40182,
"hgvs_c": "n.84-978G>T",
"hgvs_p": null,
"transcript": "ENST00000424211.1",
"protein_id": null,
"transcript_support_level": 2,
"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": 432,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "DLG3-AS1",
"gene_hgnc_id": 40182,
"hgvs_c": "n.134-978G>T",
"hgvs_p": null,
"transcript": "ENST00000431103.2",
"protein_id": null,
"transcript_support_level": 3,
"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": 484,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "DLG3-AS1",
"gene_hgnc_id": 40182,
"hgvs_c": "n.84-978G>T",
"hgvs_p": null,
"transcript": "NR_046586.1",
"protein_id": null,
"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": 434,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "DLG3-AS1",
"gene_hgnc_id": 40182,
"hgvs_c": "n.51-978G>T",
"hgvs_p": null,
"transcript": "NR_109801.1",
"protein_id": null,
"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": 401,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "DLG3",
"gene_hgnc_id": 2902,
"dbsnp": "rs398122847",
"frequency_reference_population": 9.1109365e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 9.11094e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.6200000047683716,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.7900000214576721,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.62,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.537,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.79,
"spliceai_max_prediction": "Pathogenic",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 11,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP3",
"acmg_by_gene": [
{
"score": 11,
"benign_score": 0,
"pathogenic_score": 11,
"criteria": [
"PVS1",
"PM2",
"PP3"
],
"verdict": "Pathogenic",
"transcript": "ENST00000374360.8",
"gene_symbol": "DLG3",
"hgnc_id": 2902,
"effects": [
"stop_gained"
],
"inheritance_mode": "XL",
"hgvs_c": "c.1373C>A",
"hgvs_p": "p.Ser458*"
},
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PM2",
"PP3"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000424211.1",
"gene_symbol": "DLG3-AS1",
"hgnc_id": 40182,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.84-978G>T",
"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
}