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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: 5-37816065-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=37816065&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 37816065,
"ref": "T",
"alt": "C",
"effect": "synonymous_variant",
"transcript": "NM_001190468.1",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GDNF",
"gene_hgnc_id": 4232,
"hgvs_c": "c.222A>G",
"hgvs_p": "p.Arg74Arg",
"transcript": "NM_000514.4",
"protein_id": "NP_000505.1",
"transcript_support_level": null,
"aa_start": 74,
"aa_end": null,
"aa_length": 211,
"cds_start": 222,
"cds_end": null,
"cds_length": 636,
"cdna_start": 783,
"cdna_end": null,
"cdna_length": 4171,
"mane_select": "ENST00000326524.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_000514.4"
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GDNF",
"gene_hgnc_id": 4232,
"hgvs_c": "c.222A>G",
"hgvs_p": "p.Arg74Arg",
"transcript": "ENST00000326524.7",
"protein_id": "ENSP00000317145.2",
"transcript_support_level": 1,
"aa_start": 74,
"aa_end": null,
"aa_length": 211,
"cds_start": 222,
"cds_end": null,
"cds_length": 636,
"cdna_start": 783,
"cdna_end": null,
"cdna_length": 4171,
"mane_select": "NM_000514.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000326524.7"
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GDNF",
"gene_hgnc_id": 4232,
"hgvs_c": "c.273A>G",
"hgvs_p": "p.Arg91Arg",
"transcript": "ENST00000427982.5",
"protein_id": "ENSP00000409007.1",
"transcript_support_level": 1,
"aa_start": 91,
"aa_end": null,
"aa_length": 228,
"cds_start": 273,
"cds_end": null,
"cds_length": 687,
"cdna_start": 442,
"cdna_end": null,
"cdna_length": 856,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000427982.5"
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GDNF",
"gene_hgnc_id": 4232,
"hgvs_c": "c.195A>G",
"hgvs_p": "p.Arg65Arg",
"transcript": "ENST00000381826.8",
"protein_id": "ENSP00000371248.4",
"transcript_support_level": 1,
"aa_start": 65,
"aa_end": null,
"aa_length": 202,
"cds_start": 195,
"cds_end": null,
"cds_length": 609,
"cdna_start": 364,
"cdna_end": null,
"cdna_length": 778,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000381826.8"
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GDNF",
"gene_hgnc_id": 4232,
"hgvs_c": "c.144A>G",
"hgvs_p": "p.Arg48Arg",
"transcript": "ENST00000344622.8",
"protein_id": "ENSP00000339703.4",
"transcript_support_level": 1,
"aa_start": 48,
"aa_end": null,
"aa_length": 185,
"cds_start": 144,
"cds_end": null,
"cds_length": 558,
"cdna_start": 267,
"cdna_end": null,
"cdna_length": 3655,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000344622.8"
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GDNF",
"gene_hgnc_id": 4232,
"hgvs_c": "c.66A>G",
"hgvs_p": "p.Arg22Arg",
"transcript": "ENST00000620847.1",
"protein_id": "ENSP00000478722.1",
"transcript_support_level": 1,
"aa_start": 22,
"aa_end": null,
"aa_length": 159,
"cds_start": 66,
"cds_end": null,
"cds_length": 480,
"cdna_start": 250,
"cdna_end": null,
"cdna_length": 3638,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000620847.1"
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GDNF",
"gene_hgnc_id": 4232,
"hgvs_c": "c.144A>G",
"hgvs_p": "p.Arg48Arg",
"transcript": "ENST00000502572.1",
"protein_id": "ENSP00000423557.1",
"transcript_support_level": 1,
"aa_start": 48,
"aa_end": null,
"aa_length": 60,
"cds_start": 144,
"cds_end": null,
"cds_length": 183,
"cdna_start": 267,
"cdna_end": null,
"cdna_length": 306,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000502572.1"
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GDNF",
"gene_hgnc_id": 4232,
"hgvs_c": "c.144A>G",
"hgvs_p": "p.Arg48Arg",
"transcript": "ENST00000510177.5",
"protein_id": "ENSP00000424592.1",
"transcript_support_level": 1,
"aa_start": 48,
"aa_end": null,
"aa_length": 60,
"cds_start": 144,
"cds_end": null,
"cds_length": 183,
"cdna_start": 256,
"cdna_end": null,
"cdna_length": 295,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000510177.5"
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GDNF",
"gene_hgnc_id": 4232,
"hgvs_c": "c.273A>G",
"hgvs_p": "p.Arg91Arg",
"transcript": "NM_001190468.1",
"protein_id": "NP_001177397.1",
"transcript_support_level": null,
"aa_start": 91,
"aa_end": null,
"aa_length": 228,
"cds_start": 273,
"cds_end": null,
"cds_length": 687,
"cdna_start": 442,
"cdna_end": null,
"cdna_length": 3830,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001190468.1"
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GDNF",
"gene_hgnc_id": 4232,
"hgvs_c": "c.222A>G",
"hgvs_p": "p.Arg74Arg",
"transcript": "ENST00000854000.1",
"protein_id": "ENSP00000524059.1",
"transcript_support_level": null,
"aa_start": 74,
"aa_end": null,
"aa_length": 211,
"cds_start": 222,
"cds_end": null,
"cds_length": 636,
"cdna_start": 298,
"cdna_end": null,
"cdna_length": 2802,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000854000.1"
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GDNF",
"gene_hgnc_id": 4232,
"hgvs_c": "c.195A>G",
"hgvs_p": "p.Arg65Arg",
"transcript": "NM_001190469.1",
"protein_id": "NP_001177398.1",
"transcript_support_level": null,
"aa_start": 65,
"aa_end": null,
"aa_length": 202,
"cds_start": 195,
"cds_end": null,
"cds_length": 609,
"cdna_start": 364,
"cdna_end": null,
"cdna_length": 3752,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001190469.1"
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GDNF",
"gene_hgnc_id": 4232,
"hgvs_c": "c.144A>G",
"hgvs_p": "p.Arg48Arg",
"transcript": "NM_199231.2",
"protein_id": "NP_954701.1",
"transcript_support_level": null,
"aa_start": 48,
"aa_end": null,
"aa_length": 185,
"cds_start": 144,
"cds_end": null,
"cds_length": 558,
"cdna_start": 267,
"cdna_end": null,
"cdna_length": 3655,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_199231.2"
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GDNF",
"gene_hgnc_id": 4232,
"hgvs_c": "c.144A>G",
"hgvs_p": "p.Arg48Arg",
"transcript": "ENST00000515058.5",
"protein_id": "ENSP00000425928.1",
"transcript_support_level": 5,
"aa_start": 48,
"aa_end": null,
"aa_length": 185,
"cds_start": 144,
"cds_end": null,
"cds_length": 558,
"cdna_start": 350,
"cdna_end": null,
"cdna_length": 764,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000515058.5"
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GDNF",
"gene_hgnc_id": 4232,
"hgvs_c": "c.66A>G",
"hgvs_p": "p.Arg22Arg",
"transcript": "NM_001278098.1",
"protein_id": "NP_001265027.1",
"transcript_support_level": null,
"aa_start": 22,
"aa_end": null,
"aa_length": 159,
"cds_start": 66,
"cds_end": null,
"cds_length": 480,
"cdna_start": 250,
"cdna_end": null,
"cdna_length": 3638,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001278098.1"
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GDNF",
"gene_hgnc_id": 4232,
"hgvs_c": "c.144A>G",
"hgvs_p": "p.Arg48Arg",
"transcript": "XM_017009337.3",
"protein_id": "XP_016864826.1",
"transcript_support_level": null,
"aa_start": 48,
"aa_end": null,
"aa_length": 185,
"cds_start": 144,
"cds_end": null,
"cds_length": 558,
"cdna_start": 705,
"cdna_end": null,
"cdna_length": 4093,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017009337.3"
},
{
"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": 12,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "GDNF-AS1",
"gene_hgnc_id": 43592,
"hgvs_c": "n.720+1121T>C",
"hgvs_p": null,
"transcript": "ENST00000637595.1",
"protein_id": null,
"transcript_support_level": 5,
"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": 1886,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000637595.1"
}
],
"gene_symbol": "GDNF",
"gene_hgnc_id": 4232,
"dbsnp": "rs139694199",
"frequency_reference_population": 0.00002230992,
"hom_count_reference_population": 0,
"allele_count_reference_population": 36,
"gnomad_exomes_af": 0.00000958052,
"gnomad_genomes_af": 0.000144419,
"gnomad_exomes_ac": 14,
"gnomad_genomes_ac": 22,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.6200000047683716,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.62,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.055,
"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": -17,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BS2",
"acmg_by_gene": [
{
"score": -17,
"benign_score": 17,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_001190468.1",
"gene_symbol": "GDNF",
"hgnc_id": 4232,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.273A>G",
"hgvs_p": "p.Arg91Arg"
},
{
"score": -12,
"benign_score": 12,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong"
],
"verdict": "Benign",
"transcript": "ENST00000637595.1",
"gene_symbol": "GDNF-AS1",
"hgnc_id": 43592,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.720+1121T>C",
"hgvs_p": null
}
],
"clinvar_disease": " 3, susceptibility to,GDNF-related disorder,Hirschsprung disease,not provided,not specified",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:3",
"phenotype_combined": "not specified|not provided|Hirschsprung disease, susceptibility to, 3|GDNF-related disorder",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}