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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: 18-46680195-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=18&pos=46680195&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 1,
"criteria": [
"PM2",
"BP4"
],
"effects": [
"missense_variant"
],
"gene_symbol": "ST8SIA5",
"hgnc_id": 17827,
"hgvs_c": "c.1086G>A",
"hgvs_p": "p.Met362Ile",
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": 1,
"transcript": "NM_001307986.2",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4",
"acmg_score": 1,
"allele_count_reference_population": 7,
"alphamissense_prediction": null,
"alphamissense_score": 0.6675,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.3,
"chr": "18",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.4152280390262604,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 376,
"aa_ref": "M",
"aa_start": 326,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 13897,
"cdna_start": 1523,
"cds_end": null,
"cds_length": 1131,
"cds_start": 978,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "NM_013305.6",
"gene_hgnc_id": 17827,
"gene_symbol": "ST8SIA5",
"hgvs_c": "c.978G>A",
"hgvs_p": "p.Met326Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000315087.12",
"protein_coding": true,
"protein_id": "NP_037437.2",
"strand": false,
"transcript": "NM_013305.6",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 376,
"aa_ref": "M",
"aa_start": 326,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 13897,
"cdna_start": 1523,
"cds_end": null,
"cds_length": 1131,
"cds_start": 978,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000315087.12",
"gene_hgnc_id": 17827,
"gene_symbol": "ST8SIA5",
"hgvs_c": "c.978G>A",
"hgvs_p": "p.Met326Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_013305.6",
"protein_coding": true,
"protein_id": "ENSP00000321343.6",
"strand": false,
"transcript": "ENST00000315087.12",
"transcript_support_level": 1
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 412,
"aa_ref": "M",
"aa_start": 362,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 14005,
"cdna_start": 1631,
"cds_end": null,
"cds_length": 1239,
"cds_start": 1086,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "NM_001307986.2",
"gene_hgnc_id": 17827,
"gene_symbol": "ST8SIA5",
"hgvs_c": "c.1086G>A",
"hgvs_p": "p.Met362Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001294915.1",
"strand": false,
"transcript": "NM_001307986.2",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 412,
"aa_ref": "M",
"aa_start": 362,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 13761,
"cdna_start": 1387,
"cds_end": null,
"cds_length": 1239,
"cds_start": 1086,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000538168.5",
"gene_hgnc_id": 17827,
"gene_symbol": "ST8SIA5",
"hgvs_c": "c.1086G>A",
"hgvs_p": "p.Met362Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000445492.1",
"strand": false,
"transcript": "ENST00000538168.5",
"transcript_support_level": 2
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 407,
"aa_ref": "M",
"aa_start": 357,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2472,
"cdna_start": 1401,
"cds_end": null,
"cds_length": 1224,
"cds_start": 1071,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000911623.1",
"gene_hgnc_id": 17827,
"gene_symbol": "ST8SIA5",
"hgvs_c": "c.1071G>A",
"hgvs_p": "p.Met357Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000581682.1",
"strand": false,
"transcript": "ENST00000911623.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 381,
"aa_ref": "M",
"aa_start": 331,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2251,
"cdna_start": 1298,
"cds_end": null,
"cds_length": 1146,
"cds_start": 993,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000906003.1",
"gene_hgnc_id": 17827,
"gene_symbol": "ST8SIA5",
"hgvs_c": "c.993G>A",
"hgvs_p": "p.Met331Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000576062.1",
"strand": false,
"transcript": "ENST00000906003.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 371,
"aa_ref": "M",
"aa_start": 321,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2454,
"cdna_start": 1502,
"cds_end": null,
"cds_length": 1116,
"cds_start": 963,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000951068.1",
"gene_hgnc_id": 17827,
"gene_symbol": "ST8SIA5",
"hgvs_c": "c.963G>A",
"hgvs_p": "p.Met321Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000621127.1",
"strand": false,
"transcript": "ENST00000951068.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 345,
"aa_ref": "M",
"aa_start": 295,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 13804,
"cdna_start": 1430,
"cds_end": null,
"cds_length": 1038,
"cds_start": 885,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "NM_001307987.2",
"gene_hgnc_id": 17827,
"gene_symbol": "ST8SIA5",
"hgvs_c": "c.885G>A",
"hgvs_p": "p.Met295Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001294916.1",
"strand": false,
"transcript": "NM_001307987.2",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 345,
"aa_ref": "M",
"aa_start": 295,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1499,
"cdna_start": 1187,
"cds_end": null,
"cds_length": 1038,
"cds_start": 885,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000536490.1",
"gene_hgnc_id": 17827,
"gene_symbol": "ST8SIA5",
"hgvs_c": "c.885G>A",
"hgvs_p": "p.Met295Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000443683.1",
"strand": false,
"transcript": "ENST00000536490.1",
"transcript_support_level": 2
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 261,
"aa_ref": "M",
"aa_start": 211,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2125,
"cdna_start": 1172,
"cds_end": null,
"cds_length": 786,
"cds_start": 633,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000906002.1",
"gene_hgnc_id": 17827,
"gene_symbol": "ST8SIA5",
"hgvs_c": "c.633G>A",
"hgvs_p": "p.Met211Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000576061.1",
"strand": false,
"transcript": "ENST00000906002.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 230,
"aa_ref": "M",
"aa_start": 180,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2051,
"cdna_start": 1085,
"cds_end": null,
"cds_length": 693,
"cds_start": 540,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000906001.1",
"gene_hgnc_id": 17827,
"gene_symbol": "ST8SIA5",
"hgvs_c": "c.540G>A",
"hgvs_p": "p.Met180Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000576060.1",
"strand": false,
"transcript": "ENST00000906001.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 2094,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 9,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000590497.5",
"gene_hgnc_id": 17827,
"gene_symbol": "ST8SIA5",
"hgvs_c": "n.1142G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000590497.5",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 556,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000587428.1",
"gene_hgnc_id": 17827,
"gene_symbol": "ST8SIA5",
"hgvs_c": "n.*173G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000587428.1",
"transcript_support_level": 3
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs138190768",
"effect": "missense_variant",
"frequency_reference_population": 0.0000043368573,
"gene_hgnc_id": 17827,
"gene_symbol": "ST8SIA5",
"gnomad_exomes_ac": 4,
"gnomad_exomes_af": 0.00000273621,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 3,
"gnomad_genomes_af": 0.0000197117,
"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": "not specified",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 6.119,
"pos": 46680195,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.175,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_001307986.2"
}
]
}