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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: 1-173903942-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=173903942&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 173903942,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000367698.4",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "S",
"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.1342C>T",
"hgvs_p": "p.Pro448Ser",
"transcript": "NM_000488.4",
"protein_id": "NP_000479.1",
"transcript_support_level": null,
"aa_start": 448,
"aa_end": null,
"aa_length": 464,
"cds_start": 1342,
"cds_end": null,
"cds_length": 1395,
"cdna_start": 1410,
"cdna_end": null,
"cdna_length": 1552,
"mane_select": "ENST00000367698.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"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.1342C>T",
"hgvs_p": "p.Pro448Ser",
"transcript": "ENST00000367698.4",
"protein_id": "ENSP00000356671.3",
"transcript_support_level": 1,
"aa_start": 448,
"aa_end": null,
"aa_length": 464,
"cds_start": 1342,
"cds_end": null,
"cds_length": 1395,
"cdna_start": 1410,
"cdna_end": null,
"cdna_length": 1552,
"mane_select": "NM_000488.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"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.1465C>T",
"hgvs_p": "p.Pro489Ser",
"transcript": "NM_001386302.1",
"protein_id": "NP_001373231.1",
"transcript_support_level": null,
"aa_start": 489,
"aa_end": null,
"aa_length": 505,
"cds_start": 1465,
"cds_end": null,
"cds_length": 1518,
"cdna_start": 1533,
"cdna_end": null,
"cdna_length": 1675,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"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.1423C>T",
"hgvs_p": "p.Pro475Ser",
"transcript": "NM_001386303.1",
"protein_id": "NP_001373232.1",
"transcript_support_level": null,
"aa_start": 475,
"aa_end": null,
"aa_length": 491,
"cds_start": 1423,
"cds_end": null,
"cds_length": 1476,
"cdna_start": 1491,
"cdna_end": null,
"cdna_length": 1633,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"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.1321C>T",
"hgvs_p": "p.Pro441Ser",
"transcript": "NM_001386304.1",
"protein_id": "NP_001373233.1",
"transcript_support_level": null,
"aa_start": 441,
"aa_end": null,
"aa_length": 457,
"cds_start": 1321,
"cds_end": null,
"cds_length": 1374,
"cdna_start": 1389,
"cdna_end": null,
"cdna_length": 1531,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"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.1285C>T",
"hgvs_p": "p.Pro429Ser",
"transcript": "NM_001386305.1",
"protein_id": "NP_001373234.1",
"transcript_support_level": null,
"aa_start": 429,
"aa_end": null,
"aa_length": 445,
"cds_start": 1285,
"cds_end": null,
"cds_length": 1338,
"cdna_start": 1353,
"cdna_end": null,
"cdna_length": 1495,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"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.1198C>T",
"hgvs_p": "p.Pro400Ser",
"transcript": "NM_001365052.2",
"protein_id": "NP_001351981.1",
"transcript_support_level": null,
"aa_start": 400,
"aa_end": null,
"aa_length": 416,
"cds_start": 1198,
"cds_end": null,
"cds_length": 1251,
"cdna_start": 1579,
"cdna_end": null,
"cdna_length": 1721,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"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.1126C>T",
"hgvs_p": "p.Pro376Ser",
"transcript": "NM_001386306.1",
"protein_id": "NP_001373235.1",
"transcript_support_level": null,
"aa_start": 376,
"aa_end": null,
"aa_length": 392,
"cds_start": 1126,
"cds_end": null,
"cds_length": 1179,
"cdna_start": 1194,
"cdna_end": null,
"cdna_length": 1336,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SERPINC1",
"gene_hgnc_id": 775,
"dbsnp": "rs376029223",
"frequency_reference_population": 0.00003283771,
"hom_count_reference_population": 0,
"allele_count_reference_population": 53,
"gnomad_exomes_af": 0.0000348876,
"gnomad_genomes_af": 0.0000131439,
"gnomad_exomes_ac": 51,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.049782514572143555,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.15,
"revel_prediction": "Benign",
"alphamissense_score": 0.0608,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.45,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.117,
"phylop100way_prediction": "Benign",
"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": -1,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM1,PP2,BP4_Strong",
"acmg_by_gene": [
{
"score": -1,
"benign_score": 4,
"pathogenic_score": 3,
"criteria": [
"PM1",
"PP2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "ENST00000367698.4",
"gene_symbol": "SERPINC1",
"hgnc_id": 775,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR,SD",
"hgvs_c": "c.1342C>T",
"hgvs_p": "p.Pro448Ser"
}
],
"clinvar_disease": "Hereditary antithrombin deficiency",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Hereditary antithrombin deficiency",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}