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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: 19-49650907-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=49650907&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 49650907,
"ref": "G",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_021228.3",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCAF1",
"gene_hgnc_id": 30403,
"hgvs_c": "c.518G>C",
"hgvs_p": "p.Arg173Pro",
"transcript": "NM_021228.3",
"protein_id": "NP_067051.2",
"transcript_support_level": null,
"aa_start": 173,
"aa_end": null,
"aa_length": 1312,
"cds_start": 518,
"cds_end": null,
"cds_length": 3939,
"cdna_start": 558,
"cdna_end": null,
"cdna_length": 4222,
"mane_select": "ENST00000360565.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_021228.3"
},
{
"aa_ref": "R",
"aa_alt": "P",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCAF1",
"gene_hgnc_id": 30403,
"hgvs_c": "c.518G>C",
"hgvs_p": "p.Arg173Pro",
"transcript": "ENST00000360565.8",
"protein_id": "ENSP00000353769.2",
"transcript_support_level": 2,
"aa_start": 173,
"aa_end": null,
"aa_length": 1312,
"cds_start": 518,
"cds_end": null,
"cds_length": 3939,
"cdna_start": 558,
"cdna_end": null,
"cdna_length": 4222,
"mane_select": "NM_021228.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000360565.8"
},
{
"aa_ref": "R",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCAF1",
"gene_hgnc_id": 30403,
"hgvs_c": "c.539G>C",
"hgvs_p": "p.Arg180Pro",
"transcript": "ENST00000892601.1",
"protein_id": "ENSP00000562660.1",
"transcript_support_level": null,
"aa_start": 180,
"aa_end": null,
"aa_length": 1319,
"cds_start": 539,
"cds_end": null,
"cds_length": 3960,
"cdna_start": 545,
"cdna_end": null,
"cdna_length": 4206,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000892601.1"
},
{
"aa_ref": "R",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCAF1",
"gene_hgnc_id": 30403,
"hgvs_c": "c.518G>C",
"hgvs_p": "p.Arg173Pro",
"transcript": "ENST00000892599.1",
"protein_id": "ENSP00000562658.1",
"transcript_support_level": null,
"aa_start": 173,
"aa_end": null,
"aa_length": 1312,
"cds_start": 518,
"cds_end": null,
"cds_length": 3939,
"cdna_start": 562,
"cdna_end": null,
"cdna_length": 4233,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000892599.1"
},
{
"aa_ref": "R",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCAF1",
"gene_hgnc_id": 30403,
"hgvs_c": "c.515G>C",
"hgvs_p": "p.Arg172Pro",
"transcript": "ENST00000892600.1",
"protein_id": "ENSP00000562659.1",
"transcript_support_level": null,
"aa_start": 172,
"aa_end": null,
"aa_length": 1311,
"cds_start": 515,
"cds_end": null,
"cds_length": 3936,
"cdna_start": 555,
"cdna_end": null,
"cdna_length": 4226,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000892600.1"
},
{
"aa_ref": "R",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCAF1",
"gene_hgnc_id": 30403,
"hgvs_c": "c.518G>C",
"hgvs_p": "p.Arg173Pro",
"transcript": "ENST00000598359.5",
"protein_id": "ENSP00000473210.1",
"transcript_support_level": 3,
"aa_start": 173,
"aa_end": null,
"aa_length": 202,
"cds_start": 518,
"cds_end": null,
"cds_length": 609,
"cdna_start": 571,
"cdna_end": null,
"cdna_length": 662,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000598359.5"
},
{
"aa_ref": "R",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCAF1",
"gene_hgnc_id": 30403,
"hgvs_c": "c.527G>C",
"hgvs_p": "p.Arg176Pro",
"transcript": "XM_011527194.4",
"protein_id": "XP_011525496.1",
"transcript_support_level": null,
"aa_start": 176,
"aa_end": null,
"aa_length": 1315,
"cds_start": 527,
"cds_end": null,
"cds_length": 3948,
"cdna_start": 585,
"cdna_end": null,
"cdna_length": 4249,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011527194.4"
},
{
"aa_ref": "R",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCAF1",
"gene_hgnc_id": 30403,
"hgvs_c": "c.518G>C",
"hgvs_p": "p.Arg173Pro",
"transcript": "XM_005259122.6",
"protein_id": "XP_005259179.1",
"transcript_support_level": null,
"aa_start": 173,
"aa_end": null,
"aa_length": 1312,
"cds_start": 518,
"cds_end": null,
"cds_length": 3939,
"cdna_start": 1022,
"cdna_end": null,
"cdna_length": 4686,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005259122.6"
},
{
"aa_ref": "R",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCAF1",
"gene_hgnc_id": 30403,
"hgvs_c": "c.248G>C",
"hgvs_p": "p.Arg83Pro",
"transcript": "XM_017027083.3",
"protein_id": "XP_016882572.1",
"transcript_support_level": null,
"aa_start": 83,
"aa_end": null,
"aa_length": 1222,
"cds_start": 248,
"cds_end": null,
"cds_length": 3669,
"cdna_start": 378,
"cdna_end": null,
"cdna_length": 4042,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017027083.3"
}
],
"gene_symbol": "SCAF1",
"gene_hgnc_id": 30403,
"dbsnp": "rs138080693",
"frequency_reference_population": 0.00001490424,
"hom_count_reference_population": 0,
"allele_count_reference_population": 24,
"gnomad_exomes_af": 0.00000822913,
"gnomad_genomes_af": 0.0000789235,
"gnomad_exomes_ac": 12,
"gnomad_genomes_ac": 12,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.05996394157409668,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.09000000357627869,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.16,
"revel_prediction": "Benign",
"alphamissense_score": 0.287,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.11,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.748,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.09,
"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": -4,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Strong",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "NM_021228.3",
"gene_symbol": "SCAF1",
"hgnc_id": 30403,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.518G>C",
"hgvs_p": "p.Arg173Pro"
}
],
"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
}