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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: 1-173914872-A-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=173914872&ref=A&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 173914872,
"ref": "A",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000367698.4",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SERPINC1",
"gene_hgnc_id": 775,
"hgvs_c": "c.89T>A",
"hgvs_p": "p.Val30Glu",
"transcript": "NM_000488.4",
"protein_id": "NP_000479.1",
"transcript_support_level": null,
"aa_start": 30,
"aa_end": null,
"aa_length": 464,
"cds_start": 89,
"cds_end": null,
"cds_length": 1395,
"cdna_start": 157,
"cdna_end": null,
"cdna_length": 1552,
"mane_select": "ENST00000367698.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "E",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SERPINC1",
"gene_hgnc_id": 775,
"hgvs_c": "c.89T>A",
"hgvs_p": "p.Val30Glu",
"transcript": "ENST00000367698.4",
"protein_id": "ENSP00000356671.3",
"transcript_support_level": 1,
"aa_start": 30,
"aa_end": null,
"aa_length": 464,
"cds_start": 89,
"cds_end": null,
"cds_length": 1395,
"cdna_start": 157,
"cdna_end": null,
"cdna_length": 1552,
"mane_select": "NM_000488.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SERPINC1",
"gene_hgnc_id": 775,
"hgvs_c": "c.89T>A",
"hgvs_p": "p.Val30Glu",
"transcript": "NM_001386302.1",
"protein_id": "NP_001373231.1",
"transcript_support_level": null,
"aa_start": 30,
"aa_end": null,
"aa_length": 505,
"cds_start": 89,
"cds_end": null,
"cds_length": 1518,
"cdna_start": 157,
"cdna_end": null,
"cdna_length": 1675,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SERPINC1",
"gene_hgnc_id": 775,
"hgvs_c": "c.170T>A",
"hgvs_p": "p.Val57Glu",
"transcript": "NM_001386303.1",
"protein_id": "NP_001373232.1",
"transcript_support_level": null,
"aa_start": 57,
"aa_end": null,
"aa_length": 491,
"cds_start": 170,
"cds_end": null,
"cds_length": 1476,
"cdna_start": 238,
"cdna_end": null,
"cdna_length": 1633,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SERPINC1",
"gene_hgnc_id": 775,
"hgvs_c": "c.89T>A",
"hgvs_p": "p.Val30Glu",
"transcript": "NM_001386304.1",
"protein_id": "NP_001373233.1",
"transcript_support_level": null,
"aa_start": 30,
"aa_end": null,
"aa_length": 457,
"cds_start": 89,
"cds_end": null,
"cds_length": 1374,
"cdna_start": 157,
"cdna_end": null,
"cdna_length": 1531,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SERPINC1",
"gene_hgnc_id": 775,
"hgvs_c": "c.89T>A",
"hgvs_p": "p.Val30Glu",
"transcript": "NM_001386305.1",
"protein_id": "NP_001373234.1",
"transcript_support_level": null,
"aa_start": 30,
"aa_end": null,
"aa_length": 445,
"cds_start": 89,
"cds_end": null,
"cds_length": 1338,
"cdna_start": 157,
"cdna_end": null,
"cdna_length": 1495,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SERPINC1",
"gene_hgnc_id": 775,
"hgvs_c": "c.89T>A",
"hgvs_p": "p.Val30Glu",
"transcript": "NM_001386306.1",
"protein_id": "NP_001373235.1",
"transcript_support_level": null,
"aa_start": 30,
"aa_end": null,
"aa_length": 392,
"cds_start": 89,
"cds_end": null,
"cds_length": 1179,
"cdna_start": 157,
"cdna_end": null,
"cdna_length": 1336,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SERPINC1",
"gene_hgnc_id": 775,
"hgvs_c": "n.315T>A",
"hgvs_p": null,
"transcript": "ENST00000494024.1",
"protein_id": null,
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 669,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SERPINC1",
"gene_hgnc_id": 775,
"hgvs_c": "c.-56T>A",
"hgvs_p": null,
"transcript": "NM_001365052.2",
"protein_id": "NP_001351981.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 416,
"cds_start": -4,
"cds_end": null,
"cds_length": 1251,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1721,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SERPINC1",
"gene_hgnc_id": 775,
"hgvs_c": "n.-207T>A",
"hgvs_p": null,
"transcript": "ENST00000487183.1",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 626,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SERPINC1",
"gene_hgnc_id": 775,
"dbsnp": "rs2227624",
"frequency_reference_population": 0.0026248328,
"hom_count_reference_population": 14,
"allele_count_reference_population": 4237,
"gnomad_exomes_af": 0.0027246,
"gnomad_genomes_af": 0.00166741,
"gnomad_exomes_ac": 3983,
"gnomad_genomes_ac": 254,
"gnomad_exomes_homalt": 14,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.01722201704978943,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.456,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.1217,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.21,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.818,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.01,
"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": 10,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PS3,PS4,PP1_Moderate",
"acmg_by_gene": [
{
"score": 10,
"benign_score": 0,
"pathogenic_score": 10,
"criteria": [
"PS3",
"PS4",
"PP1_Moderate"
],
"verdict": "Pathogenic",
"transcript": "ENST00000367698.4",
"gene_symbol": "SERPINC1",
"hgnc_id": 775,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR,SD",
"hgvs_c": "c.89T>A",
"hgvs_p": "p.Val30Glu"
}
],
"clinvar_disease": "Deep venous thrombosis,Hereditary antithrombin deficiency,Thromboembolism,not provided",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "reviewed by expert panel",
"clinvar_submissions_summary": "P:2 LP:1 US:5 LB:1 B:1",
"phenotype_combined": "Hereditary antithrombin deficiency|Thromboembolism|Deep venous thrombosis|not provided",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}