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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: 4-4438406-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=4438406&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 4438406,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_016930.4",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STX18",
"gene_hgnc_id": 15942,
"hgvs_c": "c.601G>A",
"hgvs_p": "p.Glu201Lys",
"transcript": "NM_016930.4",
"protein_id": "NP_058626.1",
"transcript_support_level": null,
"aa_start": 201,
"aa_end": null,
"aa_length": 335,
"cds_start": 601,
"cds_end": null,
"cds_length": 1008,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000306200.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_016930.4"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STX18",
"gene_hgnc_id": 15942,
"hgvs_c": "c.601G>A",
"hgvs_p": "p.Glu201Lys",
"transcript": "ENST00000306200.7",
"protein_id": "ENSP00000305810.2",
"transcript_support_level": 1,
"aa_start": 201,
"aa_end": null,
"aa_length": 335,
"cds_start": 601,
"cds_end": null,
"cds_length": 1008,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_016930.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000306200.7"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STX18",
"gene_hgnc_id": 15942,
"hgvs_c": "c.601G>A",
"hgvs_p": "p.Glu201Lys",
"transcript": "ENST00000505286.5",
"protein_id": "ENSP00000426648.1",
"transcript_support_level": 1,
"aa_start": 201,
"aa_end": null,
"aa_length": 308,
"cds_start": 601,
"cds_end": null,
"cds_length": 927,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000505286.5"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STX18",
"gene_hgnc_id": 15942,
"hgvs_c": "c.694G>A",
"hgvs_p": "p.Glu232Lys",
"transcript": "ENST00000963664.1",
"protein_id": "ENSP00000633723.1",
"transcript_support_level": null,
"aa_start": 232,
"aa_end": null,
"aa_length": 366,
"cds_start": 694,
"cds_end": null,
"cds_length": 1101,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000963664.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STX18",
"gene_hgnc_id": 15942,
"hgvs_c": "c.601G>A",
"hgvs_p": "p.Glu201Lys",
"transcript": "ENST00000889601.1",
"protein_id": "ENSP00000559660.1",
"transcript_support_level": null,
"aa_start": 201,
"aa_end": null,
"aa_length": 348,
"cds_start": 601,
"cds_end": null,
"cds_length": 1047,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000889601.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STX18",
"gene_hgnc_id": 15942,
"hgvs_c": "c.622G>A",
"hgvs_p": "p.Glu208Lys",
"transcript": "ENST00000889602.1",
"protein_id": "ENSP00000559661.1",
"transcript_support_level": null,
"aa_start": 208,
"aa_end": null,
"aa_length": 342,
"cds_start": 622,
"cds_end": null,
"cds_length": 1029,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000889602.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STX18",
"gene_hgnc_id": 15942,
"hgvs_c": "c.601G>A",
"hgvs_p": "p.Glu201Lys",
"transcript": "ENST00000889600.1",
"protein_id": "ENSP00000559659.1",
"transcript_support_level": null,
"aa_start": 201,
"aa_end": null,
"aa_length": 292,
"cds_start": 601,
"cds_end": null,
"cds_length": 879,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000889600.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STX18",
"gene_hgnc_id": 15942,
"hgvs_c": "c.358G>A",
"hgvs_p": "p.Glu120Lys",
"transcript": "NM_001346282.2",
"protein_id": "NP_001333211.1",
"transcript_support_level": null,
"aa_start": 120,
"aa_end": null,
"aa_length": 254,
"cds_start": 358,
"cds_end": null,
"cds_length": 765,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001346282.2"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STX18",
"gene_hgnc_id": 15942,
"hgvs_c": "c.358G>A",
"hgvs_p": "p.Glu120Lys",
"transcript": "NM_001346300.2",
"protein_id": "NP_001333229.1",
"transcript_support_level": null,
"aa_start": 120,
"aa_end": null,
"aa_length": 254,
"cds_start": 358,
"cds_end": null,
"cds_length": 765,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001346300.2"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STX18",
"gene_hgnc_id": 15942,
"hgvs_c": "c.358G>A",
"hgvs_p": "p.Glu120Lys",
"transcript": "ENST00000507908.5",
"protein_id": "ENSP00000422376.1",
"transcript_support_level": 3,
"aa_start": 120,
"aa_end": null,
"aa_length": 168,
"cds_start": 358,
"cds_end": null,
"cds_length": 509,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000507908.5"
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STX18",
"gene_hgnc_id": 15942,
"hgvs_c": "c.654G>A",
"hgvs_p": "p.Leu218Leu",
"transcript": "ENST00000963665.1",
"protein_id": "ENSP00000633724.1",
"transcript_support_level": null,
"aa_start": 218,
"aa_end": null,
"aa_length": 346,
"cds_start": 654,
"cds_end": null,
"cds_length": 1041,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000963665.1"
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STX18",
"gene_hgnc_id": 15942,
"hgvs_c": "c.654G>A",
"hgvs_p": "p.Leu218Leu",
"transcript": "NM_001346281.2",
"protein_id": "NP_001333210.1",
"transcript_support_level": null,
"aa_start": 218,
"aa_end": null,
"aa_length": 333,
"cds_start": 654,
"cds_end": null,
"cds_length": 1002,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001346281.2"
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STX18",
"gene_hgnc_id": 15942,
"hgvs_c": "c.654G>A",
"hgvs_p": "p.Leu218Leu",
"transcript": "ENST00000889603.1",
"protein_id": "ENSP00000559662.1",
"transcript_support_level": null,
"aa_start": 218,
"aa_end": null,
"aa_length": 333,
"cds_start": 654,
"cds_end": null,
"cds_length": 1002,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000889603.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STX18",
"gene_hgnc_id": 15942,
"hgvs_c": "n.401G>A",
"hgvs_p": null,
"transcript": "ENST00000503861.5",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000503861.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STX18",
"gene_hgnc_id": 15942,
"hgvs_c": "n.414G>A",
"hgvs_p": null,
"transcript": "ENST00000512195.5",
"protein_id": null,
"transcript_support_level": 3,
"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": "pseudogene",
"feature": "ENST00000512195.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STX18",
"gene_hgnc_id": 15942,
"hgvs_c": "n.685G>A",
"hgvs_p": null,
"transcript": "NR_144414.2",
"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": "pseudogene",
"feature": "NR_144414.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STX18",
"gene_hgnc_id": 15942,
"hgvs_c": "n.*33G>A",
"hgvs_p": null,
"transcript": "ENST00000512780.2",
"protein_id": null,
"transcript_support_level": 3,
"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": "ENST00000512780.2"
}
],
"gene_symbol": "STX18",
"gene_hgnc_id": 15942,
"dbsnp": "rs757868590",
"frequency_reference_population": 0.0000024825476,
"hom_count_reference_population": 0,
"allele_count_reference_population": 4,
"gnomad_exomes_af": 6.85382e-7,
"gnomad_genomes_af": 0.0000197099,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": 3,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.09804558753967285,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.149,
"revel_prediction": "Benign",
"alphamissense_score": 0.0677,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.37,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.811,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.01,
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_016930.4",
"gene_symbol": "STX18",
"hgnc_id": 15942,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.601G>A",
"hgvs_p": "p.Glu201Lys"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}