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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: 4-121681724-A-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=121681724&ref=A&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 121681724,
"ref": "A",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_001154.4",
"consequences": [
{
"aa_ref": "I",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ANXA5",
"gene_hgnc_id": 543,
"hgvs_c": "c.341T>G",
"hgvs_p": "p.Ile114Ser",
"transcript": "NM_001154.4",
"protein_id": "NP_001145.1",
"transcript_support_level": null,
"aa_start": 114,
"aa_end": null,
"aa_length": 320,
"cds_start": 341,
"cds_end": null,
"cds_length": 963,
"cdna_start": 494,
"cdna_end": null,
"cdna_length": 1638,
"mane_select": "ENST00000296511.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ANXA5",
"gene_hgnc_id": 543,
"hgvs_c": "c.341T>G",
"hgvs_p": "p.Ile114Ser",
"transcript": "ENST00000296511.10",
"protein_id": "ENSP00000296511.5",
"transcript_support_level": 1,
"aa_start": 114,
"aa_end": null,
"aa_length": 320,
"cds_start": 341,
"cds_end": null,
"cds_length": 963,
"cdna_start": 494,
"cdna_end": null,
"cdna_length": 1638,
"mane_select": "NM_001154.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ANXA5",
"gene_hgnc_id": 543,
"hgvs_c": "c.161T>G",
"hgvs_p": "p.Ile54Ser",
"transcript": "ENST00000501272.6",
"protein_id": "ENSP00000424106.1",
"transcript_support_level": 5,
"aa_start": 54,
"aa_end": null,
"aa_length": 260,
"cds_start": 161,
"cds_end": null,
"cds_length": 783,
"cdna_start": 300,
"cdna_end": null,
"cdna_length": 1363,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ANXA5",
"gene_hgnc_id": 543,
"hgvs_c": "c.341T>G",
"hgvs_p": "p.Ile114Ser",
"transcript": "XM_017008141.3",
"protein_id": "XP_016863630.1",
"transcript_support_level": null,
"aa_start": 114,
"aa_end": null,
"aa_length": 148,
"cds_start": 341,
"cds_end": null,
"cds_length": 447,
"cdna_start": 494,
"cdna_end": null,
"cdna_length": 2941,
"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": 6,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ANXA5",
"gene_hgnc_id": 543,
"hgvs_c": "n.341T>G",
"hgvs_p": null,
"transcript": "ENST00000506395.5",
"protein_id": "ENSP00000421421.1",
"transcript_support_level": 5,
"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": 1606,
"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": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ANXA5",
"gene_hgnc_id": 543,
"hgvs_c": "n.462T>G",
"hgvs_p": null,
"transcript": "ENST00000509016.5",
"protein_id": null,
"transcript_support_level": 4,
"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": 556,
"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": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ANXA5",
"gene_hgnc_id": 543,
"hgvs_c": "n.727T>G",
"hgvs_p": null,
"transcript": "ENST00000511552.5",
"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": 1036,
"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": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ANXA5",
"gene_hgnc_id": 543,
"hgvs_c": "n.506T>G",
"hgvs_p": null,
"transcript": "ENST00000513428.5",
"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": 868,
"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": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ANXA5",
"gene_hgnc_id": 543,
"hgvs_c": "n.414T>G",
"hgvs_p": null,
"transcript": "ENST00000513523.1",
"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": 582,
"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": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ANXA5",
"gene_hgnc_id": 543,
"hgvs_c": "n.*138T>G",
"hgvs_p": null,
"transcript": "ENST00000513728.1",
"protein_id": "ENSP00000427135.1",
"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": 447,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ANXA5",
"gene_hgnc_id": 543,
"hgvs_c": "n.*138T>G",
"hgvs_p": null,
"transcript": "ENST00000513728.1",
"protein_id": "ENSP00000427135.1",
"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": 447,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "ANXA5",
"gene_hgnc_id": 543,
"hgvs_c": "c.95-3230T>G",
"hgvs_p": null,
"transcript": "ENST00000515017.5",
"protein_id": "ENSP00000424199.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 220,
"cds_start": -4,
"cds_end": null,
"cds_length": 663,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1190,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ANXA5",
"gene_hgnc_id": 543,
"dbsnp": "rs199976717",
"frequency_reference_population": 0.000008899903,
"hom_count_reference_population": 0,
"allele_count_reference_population": 13,
"gnomad_exomes_af": 0.0000088999,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 13,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8519681692123413,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.391,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.8209,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.03,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 6.074,
"phylop100way_prediction": "Uncertain_significance",
"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": 4,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3_Moderate",
"acmg_by_gene": [
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_001154.4",
"gene_symbol": "ANXA5",
"hgnc_id": 543,
"effects": [
"missense_variant"
],
"inheritance_mode": "Unknown",
"hgvs_c": "c.341T>G",
"hgvs_p": "p.Ile114Ser"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}