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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: 19-6718135-T-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=6718135&ref=T&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 6718135,
"ref": "T",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000245907.11",
"consequences": [
{
"aa_ref": "K",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 41,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "C3",
"gene_hgnc_id": 1318,
"hgvs_c": "c.463A>C",
"hgvs_p": "p.Lys155Gln",
"transcript": "NM_000064.4",
"protein_id": "NP_000055.2",
"transcript_support_level": null,
"aa_start": 155,
"aa_end": null,
"aa_length": 1663,
"cds_start": 463,
"cds_end": null,
"cds_length": 4992,
"cdna_start": 524,
"cdna_end": null,
"cdna_length": 5231,
"mane_select": "ENST00000245907.11",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 41,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "C3",
"gene_hgnc_id": 1318,
"hgvs_c": "c.463A>C",
"hgvs_p": "p.Lys155Gln",
"transcript": "ENST00000245907.11",
"protein_id": "ENSP00000245907.4",
"transcript_support_level": 1,
"aa_start": 155,
"aa_end": null,
"aa_length": 1663,
"cds_start": 463,
"cds_end": null,
"cds_length": 4992,
"cdna_start": 524,
"cdna_end": null,
"cdna_length": 5231,
"mane_select": "NM_000064.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "C3",
"gene_hgnc_id": 1318,
"hgvs_c": "c.340A>C",
"hgvs_p": "p.Lys114Gln",
"transcript": "ENST00000695652.1",
"protein_id": "ENSP00000512083.1",
"transcript_support_level": null,
"aa_start": 114,
"aa_end": null,
"aa_length": 1228,
"cds_start": 340,
"cds_end": null,
"cds_length": 3687,
"cdna_start": 790,
"cdna_end": null,
"cdna_length": 4137,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "C3",
"gene_hgnc_id": 1318,
"hgvs_c": "c.463A>C",
"hgvs_p": "p.Lys155Gln",
"transcript": "ENST00000695693.1",
"protein_id": "ENSP00000512104.1",
"transcript_support_level": null,
"aa_start": 155,
"aa_end": null,
"aa_length": 210,
"cds_start": 463,
"cds_end": null,
"cds_length": 633,
"cdna_start": 509,
"cdna_end": null,
"cdna_length": 694,
"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": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "C3",
"gene_hgnc_id": 1318,
"hgvs_c": "n.524A>C",
"hgvs_p": null,
"transcript": "ENST00000594936.2",
"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": 2273,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "C3",
"gene_hgnc_id": 1318,
"hgvs_c": "c.*112A>C",
"hgvs_p": null,
"transcript": "ENST00000600744.1",
"protein_id": "ENSP00000472044.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 102,
"cds_start": -4,
"cds_end": null,
"cds_length": 310,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 708,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "C3",
"gene_hgnc_id": 1318,
"dbsnp": "rs147859257",
"frequency_reference_population": 0.003794722,
"hom_count_reference_population": 18,
"allele_count_reference_population": 6125,
"gnomad_exomes_af": 0.00394082,
"gnomad_genomes_af": 0.0023915,
"gnomad_exomes_ac": 5761,
"gnomad_genomes_ac": 364,
"gnomad_exomes_homalt": 18,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.01033109426498413,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.067,
"revel_prediction": "Benign",
"alphamissense_score": 0.092,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.44,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.762,
"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": -11,
"acmg_classification": "Benign",
"acmg_criteria": "PM1,BP4_Strong,BP6,BS1,BS2",
"acmg_by_gene": [
{
"score": -11,
"benign_score": 13,
"pathogenic_score": 2,
"criteria": [
"PM1",
"BP4_Strong",
"BP6",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000245907.11",
"gene_symbol": "C3",
"hgnc_id": 1318,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.463A>C",
"hgvs_p": "p.Lys155Gln"
}
],
"clinvar_disease": " 9, AGE-RELATED, SUSCEPTIBILITY TO,Age related macular degeneration 9,Atypical hemolytic-uremic syndrome with C3 anomaly,C3-related disorder,Complement component 3 deficiency,MACULAR DEGENERATION,Retinal dystrophy,not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:4 LB:2 B:2",
"phenotype_combined": "MACULAR DEGENERATION, AGE-RELATED, 9, SUSCEPTIBILITY TO|not specified|Age related macular degeneration 9;Complement component 3 deficiency;Atypical hemolytic-uremic syndrome with C3 anomaly|Atypical hemolytic-uremic syndrome with C3 anomaly|not provided|Complement component 3 deficiency|Age related macular degeneration 9|Retinal dystrophy|C3-related disorder",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}