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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: 1-173904007-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=173904007&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 173904007,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_000488.4",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SERPINC1",
"gene_hgnc_id": 775,
"hgvs_c": "c.1277C>T",
"hgvs_p": "p.Ser426Leu",
"transcript": "NM_000488.4",
"protein_id": "NP_000479.1",
"transcript_support_level": null,
"aa_start": 426,
"aa_end": null,
"aa_length": 464,
"cds_start": 1277,
"cds_end": null,
"cds_length": 1395,
"cdna_start": 1345,
"cdna_end": null,
"cdna_length": 1552,
"mane_select": "ENST00000367698.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SERPINC1",
"gene_hgnc_id": 775,
"hgvs_c": "c.1277C>T",
"hgvs_p": "p.Ser426Leu",
"transcript": "ENST00000367698.4",
"protein_id": "ENSP00000356671.3",
"transcript_support_level": 1,
"aa_start": 426,
"aa_end": null,
"aa_length": 464,
"cds_start": 1277,
"cds_end": null,
"cds_length": 1395,
"cdna_start": 1345,
"cdna_end": null,
"cdna_length": 1552,
"mane_select": "NM_000488.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SERPINC1",
"gene_hgnc_id": 775,
"hgvs_c": "c.1400C>T",
"hgvs_p": "p.Ser467Leu",
"transcript": "NM_001386302.1",
"protein_id": "NP_001373231.1",
"transcript_support_level": null,
"aa_start": 467,
"aa_end": null,
"aa_length": 505,
"cds_start": 1400,
"cds_end": null,
"cds_length": 1518,
"cdna_start": 1468,
"cdna_end": null,
"cdna_length": 1675,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SERPINC1",
"gene_hgnc_id": 775,
"hgvs_c": "c.1358C>T",
"hgvs_p": "p.Ser453Leu",
"transcript": "NM_001386303.1",
"protein_id": "NP_001373232.1",
"transcript_support_level": null,
"aa_start": 453,
"aa_end": null,
"aa_length": 491,
"cds_start": 1358,
"cds_end": null,
"cds_length": 1476,
"cdna_start": 1426,
"cdna_end": null,
"cdna_length": 1633,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SERPINC1",
"gene_hgnc_id": 775,
"hgvs_c": "c.1256C>T",
"hgvs_p": "p.Ser419Leu",
"transcript": "NM_001386304.1",
"protein_id": "NP_001373233.1",
"transcript_support_level": null,
"aa_start": 419,
"aa_end": null,
"aa_length": 457,
"cds_start": 1256,
"cds_end": null,
"cds_length": 1374,
"cdna_start": 1324,
"cdna_end": null,
"cdna_length": 1531,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SERPINC1",
"gene_hgnc_id": 775,
"hgvs_c": "c.1220C>T",
"hgvs_p": "p.Ser407Leu",
"transcript": "NM_001386305.1",
"protein_id": "NP_001373234.1",
"transcript_support_level": null,
"aa_start": 407,
"aa_end": null,
"aa_length": 445,
"cds_start": 1220,
"cds_end": null,
"cds_length": 1338,
"cdna_start": 1288,
"cdna_end": null,
"cdna_length": 1495,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SERPINC1",
"gene_hgnc_id": 775,
"hgvs_c": "c.1133C>T",
"hgvs_p": "p.Ser378Leu",
"transcript": "NM_001365052.2",
"protein_id": "NP_001351981.1",
"transcript_support_level": null,
"aa_start": 378,
"aa_end": null,
"aa_length": 416,
"cds_start": 1133,
"cds_end": null,
"cds_length": 1251,
"cdna_start": 1514,
"cdna_end": null,
"cdna_length": 1721,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SERPINC1",
"gene_hgnc_id": 775,
"hgvs_c": "c.1061C>T",
"hgvs_p": "p.Ser354Leu",
"transcript": "NM_001386306.1",
"protein_id": "NP_001373235.1",
"transcript_support_level": null,
"aa_start": 354,
"aa_end": null,
"aa_length": 392,
"cds_start": 1061,
"cds_end": null,
"cds_length": 1179,
"cdna_start": 1129,
"cdna_end": null,
"cdna_length": 1336,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SERPINC1",
"gene_hgnc_id": 775,
"dbsnp": "rs121909550",
"frequency_reference_population": 0.0000012391389,
"hom_count_reference_population": 0,
"allele_count_reference_population": 2,
"gnomad_exomes_af": 6.8406e-7,
"gnomad_genomes_af": 0.00000657186,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9216518998146057,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.88,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.319,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.34,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 9.145,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0,
"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": 12,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM2_Supporting,PP3,PP4,PP1_Strong,PS4,PS3_Supporting",
"acmg_by_gene": [
{
"score": 12,
"benign_score": 0,
"pathogenic_score": 12,
"criteria": [
"PM2_Supporting",
"PP3",
"PP4",
"PP1_Strong",
"PS4",
"PS3_Supporting"
],
"verdict": "Pathogenic",
"transcript": "NM_000488.4",
"gene_symbol": "SERPINC1",
"hgnc_id": 775,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR,SD",
"hgvs_c": "c.1277C>T",
"hgvs_p": "p.Ser426Leu"
}
],
"clinvar_disease": "Hereditary antithrombin deficiency",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "reviewed by expert panel",
"clinvar_submissions_summary": "P:1 LP:1",
"phenotype_combined": "Hereditary antithrombin deficiency",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}