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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: 15-38351612-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=15&pos=38351612&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "SPRED1",
"hgnc_id": 20249,
"hgvs_c": "c.1283G>T",
"hgvs_p": "p.Arg428Leu",
"inheritance_mode": "AD",
"pathogenic_score": 2,
"score": 2,
"transcript": "NM_152594.3",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_score": 2,
"allele_count_reference_population": 1,
"alphamissense_prediction": "Benign",
"alphamissense_score": 0.2155,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.24,
"chr": "15",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "Cardiovascular phenotype",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Uncertain_significance",
"computational_score_selected": 0.5158969759941101,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 444,
"aa_ref": "R",
"aa_start": 428,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7270,
"cdna_start": 1633,
"cds_end": null,
"cds_length": 1335,
"cds_start": 1283,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "NM_152594.3",
"gene_hgnc_id": 20249,
"gene_symbol": "SPRED1",
"hgvs_c": "c.1283G>T",
"hgvs_p": "p.Arg428Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000299084.9",
"protein_coding": true,
"protein_id": "NP_689807.1",
"strand": true,
"transcript": "NM_152594.3",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 444,
"aa_ref": "R",
"aa_start": 428,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 7270,
"cdna_start": 1633,
"cds_end": null,
"cds_length": 1335,
"cds_start": 1283,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000299084.9",
"gene_hgnc_id": 20249,
"gene_symbol": "SPRED1",
"hgvs_c": "c.1283G>T",
"hgvs_p": "p.Arg428Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_152594.3",
"protein_coding": true,
"protein_id": "ENSP00000299084.4",
"strand": true,
"transcript": "ENST00000299084.9",
"transcript_support_level": 1
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 456,
"aa_ref": "R",
"aa_start": 440,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5083,
"cdna_start": 1761,
"cds_end": null,
"cds_length": 1371,
"cds_start": 1319,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000881380.1",
"gene_hgnc_id": 20249,
"gene_symbol": "SPRED1",
"hgvs_c": "c.1319G>T",
"hgvs_p": "p.Arg440Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000551439.1",
"strand": true,
"transcript": "ENST00000881380.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 451,
"aa_ref": "R",
"aa_start": 435,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4622,
"cdna_start": 2186,
"cds_end": null,
"cds_length": 1356,
"cds_start": 1304,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000951939.1",
"gene_hgnc_id": 20249,
"gene_symbol": "SPRED1",
"hgvs_c": "c.1304G>T",
"hgvs_p": "p.Arg435Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000621998.1",
"strand": true,
"transcript": "ENST00000951939.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 444,
"aa_ref": "R",
"aa_start": 428,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3776,
"cdna_start": 1336,
"cds_end": null,
"cds_length": 1335,
"cds_start": 1283,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000925370.1",
"gene_hgnc_id": 20249,
"gene_symbol": "SPRED1",
"hgvs_c": "c.1283G>T",
"hgvs_p": "p.Arg428Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000595429.1",
"strand": true,
"transcript": "ENST00000925370.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 442,
"aa_ref": "R",
"aa_start": 426,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4608,
"cdna_start": 2188,
"cds_end": null,
"cds_length": 1329,
"cds_start": 1277,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000881381.1",
"gene_hgnc_id": 20249,
"gene_symbol": "SPRED1",
"hgvs_c": "c.1277G>T",
"hgvs_p": "p.Arg426Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000551440.1",
"strand": true,
"transcript": "ENST00000881381.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 391,
"aa_ref": "R",
"aa_start": 375,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4546,
"cdna_start": 2109,
"cds_end": null,
"cds_length": 1176,
"cds_start": 1124,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000951938.1",
"gene_hgnc_id": 20249,
"gene_symbol": "SPRED1",
"hgvs_c": "c.1124G>T",
"hgvs_p": "p.Arg375Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000621997.1",
"strand": true,
"transcript": "ENST00000951938.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 372,
"aa_ref": "R",
"aa_start": 356,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4088,
"cdna_start": 1651,
"cds_end": null,
"cds_length": 1119,
"cds_start": 1067,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000951940.1",
"gene_hgnc_id": 20249,
"gene_symbol": "SPRED1",
"hgvs_c": "c.1067G>T",
"hgvs_p": "p.Arg356Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000621999.1",
"strand": true,
"transcript": "ENST00000951940.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 319,
"aa_ref": "R",
"aa_start": 303,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4392,
"cdna_start": 1955,
"cds_end": null,
"cds_length": 960,
"cds_start": 908,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000951937.1",
"gene_hgnc_id": 20249,
"gene_symbol": "SPRED1",
"hgvs_c": "c.908G>T",
"hgvs_p": "p.Arg303Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000621996.1",
"strand": true,
"transcript": "ENST00000951937.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 456,
"aa_ref": "R",
"aa_start": 440,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7306,
"cdna_start": 1669,
"cds_end": null,
"cds_length": 1371,
"cds_start": 1319,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "XM_005254202.4",
"gene_hgnc_id": 20249,
"gene_symbol": "SPRED1",
"hgvs_c": "c.1319G>T",
"hgvs_p": "p.Arg440Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_005254259.1",
"strand": true,
"transcript": "XM_005254202.4",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 423,
"aa_ref": "R",
"aa_start": 407,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7370,
"cdna_start": 1733,
"cds_end": null,
"cds_length": 1272,
"cds_start": 1220,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "XM_047432199.1",
"gene_hgnc_id": 20249,
"gene_symbol": "SPRED1",
"hgvs_c": "c.1220G>T",
"hgvs_p": "p.Arg407Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047288155.1",
"strand": true,
"transcript": "XM_047432199.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 423,
"aa_ref": "R",
"aa_start": 407,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7334,
"cdna_start": 1697,
"cds_end": null,
"cds_length": 1272,
"cds_start": 1220,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "XM_047432200.1",
"gene_hgnc_id": 20249,
"gene_symbol": "SPRED1",
"hgvs_c": "c.1220G>T",
"hgvs_p": "p.Arg407Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047288156.1",
"strand": true,
"transcript": "XM_047432200.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 423,
"aa_ref": "R",
"aa_start": 407,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7007,
"cdna_start": 1370,
"cds_end": null,
"cds_length": 1272,
"cds_start": 1220,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "XM_047432201.1",
"gene_hgnc_id": 20249,
"gene_symbol": "SPRED1",
"hgvs_c": "c.1220G>T",
"hgvs_p": "p.Arg407Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047288157.1",
"strand": true,
"transcript": "XM_047432201.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs369492789",
"effect": "missense_variant",
"frequency_reference_population": 0.0000065657296,
"gene_hgnc_id": 20249,
"gene_symbol": "SPRED1",
"gnomad_exomes_ac": null,
"gnomad_exomes_af": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_ac": 1,
"gnomad_genomes_af": 0.00000656573,
"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": "Cardiovascular phenotype",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 4.631,
"pos": 38351612,
"ref": "G",
"revel_prediction": "Benign",
"revel_score": 0.26,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_152594.3"
}
]
}