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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: 19-1399013-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=1399013&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM1",
"PM2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "GAMT",
"hgnc_id": 4136,
"hgvs_c": "c.473G>A",
"hgvs_p": "p.Arg158His",
"inheritance_mode": "AR",
"pathogenic_score": 4,
"score": 4,
"transcript": "NM_138924.3",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM1,PM2",
"acmg_score": 4,
"allele_count_reference_population": 50,
"alphamissense_prediction": null,
"alphamissense_score": 0.1467,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Uncertain_significance",
"bayesdelnoaf_score": -0.02,
"chr": "19",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "Cerebral creatine deficiency syndrome,Deficiency of guanidinoacetate methyltransferase",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:2",
"computational_prediction_selected": "Uncertain_significance",
"computational_score_selected": 0.6499197483062744,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 236,
"aa_ref": "R",
"aa_start": 158,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1110,
"cdna_start": 539,
"cds_end": null,
"cds_length": 711,
"cds_start": 473,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "NM_000156.6",
"gene_hgnc_id": 4136,
"gene_symbol": "GAMT",
"hgvs_c": "c.473G>A",
"hgvs_p": "p.Arg158His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000252288.8",
"protein_coding": true,
"protein_id": "NP_000147.1",
"strand": false,
"transcript": "NM_000156.6",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 236,
"aa_ref": "R",
"aa_start": 158,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 1110,
"cdna_start": 539,
"cds_end": null,
"cds_length": 711,
"cds_start": 473,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000252288.8",
"gene_hgnc_id": 4136,
"gene_symbol": "GAMT",
"hgvs_c": "c.473G>A",
"hgvs_p": "p.Arg158His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_000156.6",
"protein_coding": true,
"protein_id": "ENSP00000252288.1",
"strand": false,
"transcript": "ENST00000252288.8",
"transcript_support_level": 1
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 326,
"aa_ref": "R",
"aa_start": 248,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1304,
"cdna_start": 801,
"cds_end": null,
"cds_length": 981,
"cds_start": 743,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000902474.1",
"gene_hgnc_id": 4136,
"gene_symbol": "GAMT",
"hgvs_c": "c.743G>A",
"hgvs_p": "p.Arg248His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000572533.1",
"strand": false,
"transcript": "ENST00000902474.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 269,
"aa_ref": "R",
"aa_start": 158,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1737,
"cdna_start": 539,
"cds_end": null,
"cds_length": 810,
"cds_start": 473,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "NM_138924.3",
"gene_hgnc_id": 4136,
"gene_symbol": "GAMT",
"hgvs_c": "c.473G>A",
"hgvs_p": "p.Arg158His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_620279.1",
"strand": false,
"transcript": "NM_138924.3",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 269,
"aa_ref": "R",
"aa_start": 158,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1769,
"cdna_start": 567,
"cds_end": null,
"cds_length": 810,
"cds_start": 473,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000447102.8",
"gene_hgnc_id": 4136,
"gene_symbol": "GAMT",
"hgvs_c": "c.473G>A",
"hgvs_p": "p.Arg158His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000403536.2",
"strand": false,
"transcript": "ENST00000447102.8",
"transcript_support_level": 2
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 237,
"aa_ref": "R",
"aa_start": 159,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1049,
"cdna_start": 542,
"cds_end": null,
"cds_length": 714,
"cds_start": 476,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000902472.1",
"gene_hgnc_id": 4136,
"gene_symbol": "GAMT",
"hgvs_c": "c.476G>A",
"hgvs_p": "p.Arg159His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000572531.1",
"strand": false,
"transcript": "ENST00000902472.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 235,
"aa_ref": "R",
"aa_start": 158,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1007,
"cdna_start": 507,
"cds_end": null,
"cds_length": 708,
"cds_start": 473,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000902476.1",
"gene_hgnc_id": 4136,
"gene_symbol": "GAMT",
"hgvs_c": "c.473G>A",
"hgvs_p": "p.Arg158His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000572535.1",
"strand": false,
"transcript": "ENST00000902476.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 232,
"aa_ref": "R",
"aa_start": 154,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1003,
"cdna_start": 500,
"cds_end": null,
"cds_length": 699,
"cds_start": 461,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000902475.1",
"gene_hgnc_id": 4136,
"gene_symbol": "GAMT",
"hgvs_c": "c.461G>A",
"hgvs_p": "p.Arg154His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000572534.1",
"strand": false,
"transcript": "ENST00000902475.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 222,
"aa_ref": "R",
"aa_start": 144,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1006,
"cdna_start": 493,
"cds_end": null,
"cds_length": 669,
"cds_start": 431,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000902471.1",
"gene_hgnc_id": 4136,
"gene_symbol": "GAMT",
"hgvs_c": "c.431G>A",
"hgvs_p": "p.Arg144His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000572530.1",
"strand": false,
"transcript": "ENST00000902471.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 213,
"aa_ref": "R",
"aa_start": 135,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 751,
"cdna_start": 422,
"cds_end": null,
"cds_length": 642,
"cds_start": 404,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000640762.1",
"gene_hgnc_id": 4136,
"gene_symbol": "GAMT",
"hgvs_c": "c.404G>A",
"hgvs_p": "p.Arg135His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000492031.1",
"strand": false,
"transcript": "ENST00000640762.1",
"transcript_support_level": 5
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 212,
"aa_ref": "R",
"aa_start": 135,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 943,
"cdna_start": 443,
"cds_end": null,
"cds_length": 639,
"cds_start": 404,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000970136.1",
"gene_hgnc_id": 4136,
"gene_symbol": "GAMT",
"hgvs_c": "c.404G>A",
"hgvs_p": "p.Arg135His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000640195.1",
"strand": false,
"transcript": "ENST00000970136.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 196,
"aa_ref": "R",
"aa_start": 118,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 948,
"cdna_start": 438,
"cds_end": null,
"cds_length": 591,
"cds_start": 353,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000902470.1",
"gene_hgnc_id": 4136,
"gene_symbol": "GAMT",
"hgvs_c": "c.353G>A",
"hgvs_p": "p.Arg118His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000572529.1",
"strand": false,
"transcript": "ENST00000902470.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 166,
"aa_ref": "R",
"aa_start": 88,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 834,
"cdna_start": 321,
"cds_end": null,
"cds_length": 501,
"cds_start": 263,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000902473.1",
"gene_hgnc_id": 4136,
"gene_symbol": "GAMT",
"hgvs_c": "c.263G>A",
"hgvs_p": "p.Arg88His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000572532.1",
"strand": false,
"transcript": "ENST00000902473.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 107,
"aa_ref": "R",
"aa_start": 52,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 401,
"cdna_start": 156,
"cds_end": null,
"cds_length": 324,
"cds_start": 155,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000591788.3",
"gene_hgnc_id": 4136,
"gene_symbol": "GAMT",
"hgvs_c": "c.155G>A",
"hgvs_p": "p.Arg52His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000466341.3",
"strand": false,
"transcript": "ENST00000591788.3",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 228,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 984,
"cdna_start": null,
"cds_end": null,
"cds_length": 687,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 6,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000902477.1",
"gene_hgnc_id": 4136,
"gene_symbol": "GAMT",
"hgvs_c": "c.460-11G>A",
"hgvs_p": null,
"intron_rank": 4,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000572536.1",
"strand": false,
"transcript": "ENST00000902477.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 520,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 4,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000640164.1",
"gene_hgnc_id": 4136,
"gene_symbol": "GAMT",
"hgvs_c": "n.306G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000640164.1",
"transcript_support_level": 2
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs750195151",
"effect": "missense_variant",
"frequency_reference_population": 0.00003099184,
"gene_hgnc_id": 4136,
"gene_symbol": "GAMT",
"gnomad_exomes_ac": 48,
"gnomad_exomes_af": 0.0000328515,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 2,
"gnomad_genomes_af": 0.0000131401,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "Cerebral creatine deficiency syndrome|Deficiency of guanidinoacetate methyltransferase",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 5.702,
"pos": 1399013,
"ref": "C",
"revel_prediction": "Uncertain_significance",
"revel_score": 0.572,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_138924.3"
}
]
}