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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: 19-46846102-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=46846102&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 46846102,
"ref": "C",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000263270.11",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP2S1",
"gene_hgnc_id": 565,
"hgvs_c": "c.44G>T",
"hgvs_p": "p.Arg15Leu",
"transcript": "NM_004069.6",
"protein_id": "NP_004060.2",
"transcript_support_level": null,
"aa_start": 15,
"aa_end": null,
"aa_length": 142,
"cds_start": 44,
"cds_end": null,
"cds_length": 429,
"cdna_start": 124,
"cdna_end": null,
"cdna_length": 789,
"mane_select": "ENST00000263270.11",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP2S1",
"gene_hgnc_id": 565,
"hgvs_c": "c.44G>T",
"hgvs_p": "p.Arg15Leu",
"transcript": "ENST00000263270.11",
"protein_id": "ENSP00000263270.6",
"transcript_support_level": 1,
"aa_start": 15,
"aa_end": null,
"aa_length": 142,
"cds_start": 44,
"cds_end": null,
"cds_length": 429,
"cdna_start": 124,
"cdna_end": null,
"cdna_length": 789,
"mane_select": "NM_004069.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP2S1",
"gene_hgnc_id": 565,
"hgvs_c": "c.-17G>T",
"hgvs_p": null,
"transcript": "ENST00000597020.5",
"protein_id": "ENSP00000470235.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 122,
"cds_start": -4,
"cds_end": null,
"cds_length": 369,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 707,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP2S1",
"gene_hgnc_id": 565,
"hgvs_c": "c.92G>T",
"hgvs_p": "p.Arg31Leu",
"transcript": "NM_001301076.3",
"protein_id": "NP_001288005.1",
"transcript_support_level": null,
"aa_start": 31,
"aa_end": null,
"aa_length": 158,
"cds_start": 92,
"cds_end": null,
"cds_length": 477,
"cdna_start": 222,
"cdna_end": null,
"cdna_length": 887,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP2S1",
"gene_hgnc_id": 565,
"hgvs_c": "c.92G>T",
"hgvs_p": "p.Arg31Leu",
"transcript": "ENST00000601498.5",
"protein_id": "ENSP00000470176.1",
"transcript_support_level": 2,
"aa_start": 31,
"aa_end": null,
"aa_length": 158,
"cds_start": 92,
"cds_end": null,
"cds_length": 477,
"cdna_start": 224,
"cdna_end": null,
"cdna_length": 898,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP2S1",
"gene_hgnc_id": 565,
"hgvs_c": "c.44G>T",
"hgvs_p": "p.Arg15Leu",
"transcript": "NM_001301078.3",
"protein_id": "NP_001288007.1",
"transcript_support_level": null,
"aa_start": 15,
"aa_end": null,
"aa_length": 156,
"cds_start": 44,
"cds_end": null,
"cds_length": 471,
"cdna_start": 124,
"cdna_end": null,
"cdna_length": 831,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP2S1",
"gene_hgnc_id": 565,
"hgvs_c": "c.44G>T",
"hgvs_p": "p.Arg15Leu",
"transcript": "ENST00000352203.8",
"protein_id": "ENSP00000263271.6",
"transcript_support_level": 2,
"aa_start": 15,
"aa_end": null,
"aa_length": 156,
"cds_start": 44,
"cds_end": null,
"cds_length": 471,
"cdna_start": 55,
"cdna_end": null,
"cdna_length": 793,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP2S1",
"gene_hgnc_id": 565,
"hgvs_c": "c.50G>T",
"hgvs_p": "p.Arg17Leu",
"transcript": "NM_001301081.3",
"protein_id": "NP_001288010.1",
"transcript_support_level": null,
"aa_start": 17,
"aa_end": null,
"aa_length": 144,
"cds_start": 50,
"cds_end": null,
"cds_length": 435,
"cdna_start": 232,
"cdna_end": null,
"cdna_length": 897,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP2S1",
"gene_hgnc_id": 565,
"hgvs_c": "c.50G>T",
"hgvs_p": "p.Arg17Leu",
"transcript": "ENST00000599990.5",
"protein_id": "ENSP00000471340.1",
"transcript_support_level": 2,
"aa_start": 17,
"aa_end": null,
"aa_length": 144,
"cds_start": 50,
"cds_end": null,
"cds_length": 435,
"cdna_start": 155,
"cdna_end": null,
"cdna_length": 829,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP2S1",
"gene_hgnc_id": 565,
"hgvs_c": "c.44G>T",
"hgvs_p": "p.Arg15Leu",
"transcript": "NM_021575.5",
"protein_id": "NP_067586.1",
"transcript_support_level": null,
"aa_start": 15,
"aa_end": null,
"aa_length": 104,
"cds_start": 44,
"cds_end": null,
"cds_length": 315,
"cdna_start": 124,
"cdna_end": null,
"cdna_length": 675,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP2S1",
"gene_hgnc_id": 565,
"hgvs_c": "c.44G>T",
"hgvs_p": "p.Arg15Leu",
"transcript": "ENST00000601649.1",
"protein_id": "ENSP00000470898.1",
"transcript_support_level": 3,
"aa_start": 15,
"aa_end": null,
"aa_length": 104,
"cds_start": 44,
"cds_end": null,
"cds_length": 315,
"cdna_start": 44,
"cdna_end": null,
"cdna_length": 315,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP2S1",
"gene_hgnc_id": 565,
"hgvs_c": "c.92G>T",
"hgvs_p": "p.Arg31Leu",
"transcript": "XM_011526423.3",
"protein_id": "XP_011524725.1",
"transcript_support_level": null,
"aa_start": 31,
"aa_end": null,
"aa_length": 172,
"cds_start": 92,
"cds_end": null,
"cds_length": 519,
"cdna_start": 387,
"cdna_end": null,
"cdna_length": 1094,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP2S1",
"gene_hgnc_id": 565,
"hgvs_c": "c.50G>T",
"hgvs_p": "p.Arg17Leu",
"transcript": "XM_011526424.4",
"protein_id": "XP_011524726.1",
"transcript_support_level": null,
"aa_start": 17,
"aa_end": null,
"aa_length": 158,
"cds_start": 50,
"cds_end": null,
"cds_length": 477,
"cdna_start": 232,
"cdna_end": null,
"cdna_length": 939,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP2S1",
"gene_hgnc_id": 565,
"hgvs_c": "n.103G>T",
"hgvs_p": null,
"transcript": "ENST00000597421.1",
"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": 554,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "AP2S1",
"gene_hgnc_id": 565,
"hgvs_c": "c.3+4662G>T",
"hgvs_p": null,
"transcript": "ENST00000593442.5",
"protein_id": "ENSP00000472080.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 92,
"cds_start": -4,
"cds_end": null,
"cds_length": 279,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 636,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "AP2S1",
"gene_hgnc_id": 565,
"dbsnp": "rs397514499",
"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": 0.9532224535942078,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.835,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.997,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.38,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.226,
"phylop100way_prediction": "Uncertain_significance",
"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": 18,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM1,PM2,PM5,PP3_Strong,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 18,
"benign_score": 0,
"pathogenic_score": 18,
"criteria": [
"PM1",
"PM2",
"PM5",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000263270.11",
"gene_symbol": "AP2S1",
"hgnc_id": 565,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.44G>T",
"hgvs_p": "p.Arg15Leu"
}
],
"clinvar_disease": "AP2S1-related disorder,Familial hypocalciuric hypercalcemia 3,not provided",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:5",
"phenotype_combined": "Familial hypocalciuric hypercalcemia 3|not provided|AP2S1-related disorder",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}