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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: 19-49646605-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=49646605&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 6,
"criteria": [
"BP4_Strong",
"BP6_Moderate"
],
"effects": [
"missense_variant"
],
"gene_symbol": "SCAF1",
"hgnc_id": 30403,
"hgvs_c": "c.341G>A",
"hgvs_p": "p.Arg114His",
"inheritance_mode": "",
"pathogenic_score": 0,
"score": -6,
"transcript": "NM_021228.3",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Strong,BP6_Moderate",
"acmg_score": -6,
"allele_count_reference_population": 202,
"alphamissense_prediction": null,
"alphamissense_score": 0.0583,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.7,
"chr": "19",
"clinvar_classification": "Likely benign",
"clinvar_disease": "not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.011184364557266235,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 1312,
"aa_ref": "R",
"aa_start": 114,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4222,
"cdna_start": 381,
"cds_end": null,
"cds_length": 3939,
"cds_start": 341,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "NM_021228.3",
"gene_hgnc_id": 30403,
"gene_symbol": "SCAF1",
"hgvs_c": "c.341G>A",
"hgvs_p": "p.Arg114His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000360565.8",
"protein_coding": true,
"protein_id": "NP_067051.2",
"strand": true,
"transcript": "NM_021228.3",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 1312,
"aa_ref": "R",
"aa_start": 114,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 4222,
"cdna_start": 381,
"cds_end": null,
"cds_length": 3939,
"cds_start": 341,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000360565.8",
"gene_hgnc_id": 30403,
"gene_symbol": "SCAF1",
"hgvs_c": "c.341G>A",
"hgvs_p": "p.Arg114His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_021228.3",
"protein_coding": true,
"protein_id": "ENSP00000353769.2",
"strand": true,
"transcript": "ENST00000360565.8",
"transcript_support_level": 2
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 1319,
"aa_ref": "R",
"aa_start": 121,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4206,
"cdna_start": 368,
"cds_end": null,
"cds_length": 3960,
"cds_start": 362,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000892601.1",
"gene_hgnc_id": 30403,
"gene_symbol": "SCAF1",
"hgvs_c": "c.362G>A",
"hgvs_p": "p.Arg121His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000562660.1",
"strand": true,
"transcript": "ENST00000892601.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 1312,
"aa_ref": "R",
"aa_start": 114,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4233,
"cdna_start": 385,
"cds_end": null,
"cds_length": 3939,
"cds_start": 341,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000892599.1",
"gene_hgnc_id": 30403,
"gene_symbol": "SCAF1",
"hgvs_c": "c.341G>A",
"hgvs_p": "p.Arg114His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000562658.1",
"strand": true,
"transcript": "ENST00000892599.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 1311,
"aa_ref": "R",
"aa_start": 114,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4226,
"cdna_start": 381,
"cds_end": null,
"cds_length": 3936,
"cds_start": 341,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000892600.1",
"gene_hgnc_id": 30403,
"gene_symbol": "SCAF1",
"hgvs_c": "c.341G>A",
"hgvs_p": "p.Arg114His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000562659.1",
"strand": true,
"transcript": "ENST00000892600.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 202,
"aa_ref": "R",
"aa_start": 114,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 662,
"cdna_start": 394,
"cds_end": null,
"cds_length": 609,
"cds_start": 341,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000598359.5",
"gene_hgnc_id": 30403,
"gene_symbol": "SCAF1",
"hgvs_c": "c.341G>A",
"hgvs_p": "p.Arg114His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000473210.1",
"strand": true,
"transcript": "ENST00000598359.5",
"transcript_support_level": 3
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 1315,
"aa_ref": "R",
"aa_start": 117,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4249,
"cdna_start": 408,
"cds_end": null,
"cds_length": 3948,
"cds_start": 350,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "XM_011527194.4",
"gene_hgnc_id": 30403,
"gene_symbol": "SCAF1",
"hgvs_c": "c.350G>A",
"hgvs_p": "p.Arg117His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011525496.1",
"strand": true,
"transcript": "XM_011527194.4",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 1312,
"aa_ref": "R",
"aa_start": 114,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4686,
"cdna_start": 845,
"cds_end": null,
"cds_length": 3939,
"cds_start": 341,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "XM_005259122.6",
"gene_hgnc_id": 30403,
"gene_symbol": "SCAF1",
"hgvs_c": "c.341G>A",
"hgvs_p": "p.Arg114His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_005259179.1",
"strand": true,
"transcript": "XM_005259122.6",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 1222,
"aa_ref": "R",
"aa_start": 24,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4042,
"cdna_start": 201,
"cds_end": null,
"cds_length": 3669,
"cds_start": 71,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "XM_017027083.3",
"gene_hgnc_id": 30403,
"gene_symbol": "SCAF1",
"hgvs_c": "c.71G>A",
"hgvs_p": "p.Arg24His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016882572.1",
"strand": true,
"transcript": "XM_017027083.3",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 118,
"aa_ref": "P",
"aa_start": 115,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 463,
"cdna_start": 449,
"cds_end": null,
"cds_length": 359,
"cds_start": 345,
"consequences": [
"synonymous_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000595242.3",
"gene_hgnc_id": 30403,
"gene_symbol": "SCAF1",
"hgvs_c": "c.345G>A",
"hgvs_p": "p.Pro115Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000472276.1",
"strand": true,
"transcript": "ENST00000595242.3",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 97,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 491,
"cdna_start": null,
"cds_end": null,
"cds_length": 294,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000601038.5",
"gene_hgnc_id": 30403,
"gene_symbol": "SCAF1",
"hgvs_c": "c.*47G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000472649.1",
"strand": true,
"transcript": "ENST00000601038.5",
"transcript_support_level": 3
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs199544813",
"effect": "missense_variant",
"frequency_reference_population": 0.00012514714,
"gene_hgnc_id": 30403,
"gene_symbol": "SCAF1",
"gnomad_exomes_ac": 171,
"gnomad_exomes_af": 0.000116979,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 31,
"gnomad_genomes_af": 0.000203554,
"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": "Likely benign",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Benign",
"phylop100way_score": 0.708,
"pos": 49646605,
"ref": "G",
"revel_prediction": "Benign",
"revel_score": 0.018,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.05000000074505806,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.05,
"transcript": "NM_021228.3"
}
]
}