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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: 6-78955243-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=78955243&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "6",
"pos": 78955243,
"ref": "G",
"alt": "A",
"effect": "stop_gained",
"transcript": "NM_017934.7",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 34,
"exon_rank_end": null,
"exon_count": 40,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHIP",
"gene_hgnc_id": 15673,
"hgvs_c": "c.3892C>T",
"hgvs_p": "p.Arg1298*",
"transcript": "NM_017934.7",
"protein_id": "NP_060404.4",
"transcript_support_level": null,
"aa_start": 1298,
"aa_end": null,
"aa_length": 1821,
"cds_start": 3892,
"cds_end": null,
"cds_length": 5466,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000275034.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_017934.7"
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 34,
"exon_rank_end": null,
"exon_count": 40,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHIP",
"gene_hgnc_id": 15673,
"hgvs_c": "c.3892C>T",
"hgvs_p": "p.Arg1298*",
"transcript": "ENST00000275034.5",
"protein_id": "ENSP00000275034.3",
"transcript_support_level": 1,
"aa_start": 1298,
"aa_end": null,
"aa_length": 1821,
"cds_start": 3892,
"cds_end": null,
"cds_length": 5466,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_017934.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000275034.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHIP",
"gene_hgnc_id": 15673,
"hgvs_c": "n.3973C>T",
"hgvs_p": null,
"transcript": "ENST00000479165.1",
"protein_id": null,
"transcript_support_level": 1,
"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": "retained_intron",
"feature": "ENST00000479165.1"
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 34,
"exon_rank_end": null,
"exon_count": 40,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHIP",
"gene_hgnc_id": 15673,
"hgvs_c": "c.3931C>T",
"hgvs_p": "p.Arg1311*",
"transcript": "ENST00000700118.1",
"protein_id": "ENSP00000514810.1",
"transcript_support_level": null,
"aa_start": 1311,
"aa_end": null,
"aa_length": 1834,
"cds_start": 3931,
"cds_end": null,
"cds_length": 5505,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000700118.1"
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 35,
"exon_rank_end": null,
"exon_count": 41,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHIP",
"gene_hgnc_id": 15673,
"hgvs_c": "c.3910C>T",
"hgvs_p": "p.Arg1304*",
"transcript": "ENST00000700013.1",
"protein_id": "ENSP00000514754.1",
"transcript_support_level": null,
"aa_start": 1304,
"aa_end": null,
"aa_length": 1827,
"cds_start": 3910,
"cds_end": null,
"cds_length": 5484,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000700013.1"
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 34,
"exon_rank_end": null,
"exon_count": 40,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHIP",
"gene_hgnc_id": 15673,
"hgvs_c": "c.3889C>T",
"hgvs_p": "p.Arg1297*",
"transcript": "ENST00000700115.1",
"protein_id": "ENSP00000514809.1",
"transcript_support_level": null,
"aa_start": 1297,
"aa_end": null,
"aa_length": 1820,
"cds_start": 3889,
"cds_end": null,
"cds_length": 5463,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000700115.1"
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 34,
"exon_rank_end": null,
"exon_count": 40,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHIP",
"gene_hgnc_id": 15673,
"hgvs_c": "c.3892C>T",
"hgvs_p": "p.Arg1298*",
"transcript": "ENST00000913657.1",
"protein_id": "ENSP00000583716.1",
"transcript_support_level": null,
"aa_start": 1298,
"aa_end": null,
"aa_length": 1820,
"cds_start": 3892,
"cds_end": null,
"cds_length": 5463,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000913657.1"
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 33,
"exon_rank_end": null,
"exon_count": 39,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHIP",
"gene_hgnc_id": 15673,
"hgvs_c": "c.3832C>T",
"hgvs_p": "p.Arg1278*",
"transcript": "ENST00000700114.1",
"protein_id": "ENSP00000514808.1",
"transcript_support_level": null,
"aa_start": 1278,
"aa_end": null,
"aa_length": 1801,
"cds_start": 3832,
"cds_end": null,
"cds_length": 5406,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000700114.1"
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 34,
"exon_rank_end": null,
"exon_count": 39,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHIP",
"gene_hgnc_id": 15673,
"hgvs_c": "c.3892C>T",
"hgvs_p": "p.Arg1298*",
"transcript": "ENST00000965196.1",
"protein_id": "ENSP00000635255.1",
"transcript_support_level": null,
"aa_start": 1298,
"aa_end": null,
"aa_length": 1770,
"cds_start": 3892,
"cds_end": null,
"cds_length": 5313,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000965196.1"
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 34,
"exon_rank_end": null,
"exon_count": 39,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHIP",
"gene_hgnc_id": 15673,
"hgvs_c": "c.3889C>T",
"hgvs_p": "p.Arg1297*",
"transcript": "ENST00000913659.1",
"protein_id": "ENSP00000583718.1",
"transcript_support_level": null,
"aa_start": 1297,
"aa_end": null,
"aa_length": 1769,
"cds_start": 3889,
"cds_end": null,
"cds_length": 5310,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000913659.1"
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 32,
"exon_rank_end": null,
"exon_count": 38,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHIP",
"gene_hgnc_id": 15673,
"hgvs_c": "c.3718C>T",
"hgvs_p": "p.Arg1240*",
"transcript": "ENST00000913660.1",
"protein_id": "ENSP00000583719.1",
"transcript_support_level": null,
"aa_start": 1240,
"aa_end": null,
"aa_length": 1763,
"cds_start": 3718,
"cds_end": null,
"cds_length": 5292,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000913660.1"
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 32,
"exon_rank_end": null,
"exon_count": 38,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHIP",
"gene_hgnc_id": 15673,
"hgvs_c": "c.3703C>T",
"hgvs_p": "p.Arg1235*",
"transcript": "ENST00000913658.1",
"protein_id": "ENSP00000583717.1",
"transcript_support_level": null,
"aa_start": 1235,
"aa_end": null,
"aa_length": 1758,
"cds_start": 3703,
"cds_end": null,
"cds_length": 5277,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000913658.1"
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 34,
"exon_rank_end": null,
"exon_count": 40,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHIP",
"gene_hgnc_id": 15673,
"hgvs_c": "c.3889C>T",
"hgvs_p": "p.Arg1297*",
"transcript": "XM_005248729.6",
"protein_id": "XP_005248786.1",
"transcript_support_level": null,
"aa_start": 1297,
"aa_end": null,
"aa_length": 1820,
"cds_start": 3889,
"cds_end": null,
"cds_length": 5463,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005248729.6"
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 31,
"exon_rank_end": null,
"exon_count": 37,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHIP",
"gene_hgnc_id": 15673,
"hgvs_c": "c.3376C>T",
"hgvs_p": "p.Arg1126*",
"transcript": "XM_011535918.4",
"protein_id": "XP_011534220.1",
"transcript_support_level": null,
"aa_start": 1126,
"aa_end": null,
"aa_length": 1649,
"cds_start": 3376,
"cds_end": null,
"cds_length": 4950,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011535918.4"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "IRAK1BP1",
"gene_hgnc_id": 17368,
"hgvs_c": "c.*37+19674G>A",
"hgvs_p": null,
"transcript": "XM_047418194.1",
"protein_id": "XP_047274150.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 150,
"cds_start": null,
"cds_end": null,
"cds_length": 453,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047418194.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHIP",
"gene_hgnc_id": 15673,
"hgvs_c": "n.2091C>T",
"hgvs_p": null,
"transcript": "ENST00000700116.1",
"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": "retained_intron",
"feature": "ENST00000700116.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHIP",
"gene_hgnc_id": 15673,
"hgvs_c": "n.540C>T",
"hgvs_p": null,
"transcript": "ENST00000700170.1",
"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": "retained_intron",
"feature": "ENST00000700170.1"
}
],
"gene_symbol": "PHIP",
"gene_hgnc_id": 15673,
"dbsnp": "rs759380520",
"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": 0.5799999833106995,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.10999999940395355,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.58,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 2.305,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.11,
"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": 18,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 18,
"benign_score": 0,
"pathogenic_score": 18,
"criteria": [
"PVS1",
"PM2",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "NM_017934.7",
"gene_symbol": "PHIP",
"hgnc_id": 15673,
"effects": [
"stop_gained"
],
"inheritance_mode": "AD",
"hgvs_c": "c.3892C>T",
"hgvs_p": "p.Arg1298*"
},
{
"score": 14,
"benign_score": 0,
"pathogenic_score": 14,
"criteria": [
"PM2",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "XM_047418194.1",
"gene_symbol": "IRAK1BP1",
"hgnc_id": 17368,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.*37+19674G>A",
"hgvs_p": null
}
],
"clinvar_disease": "Syndromic intellectual disability,not provided",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:2 LP:2",
"phenotype_combined": "Syndromic intellectual disability|not provided",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}