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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: 19-860686-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=860686&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PVS1",
"PM2",
"PP5_Moderate"
],
"effects": [
"stop_gained"
],
"gene_symbol": "CFD",
"hgnc_id": 2771,
"hgvs_c": "c.146C>A",
"hgvs_p": "p.Ser49*",
"inheritance_mode": "AR",
"pathogenic_score": 12,
"score": 12,
"transcript": "NM_001317335.2",
"verdict": "Pathogenic"
}
],
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5_Moderate",
"acmg_score": 12,
"allele_count_reference_population": 26,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.35,
"chr": "19",
"clinvar_classification": "Pathogenic",
"clinvar_disease": "Recurrent Neisseria infections due to factor D deficiency,not provided",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.3499999940395355,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 253,
"aa_ref": "S",
"aa_start": 42,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1191,
"cdna_start": 151,
"cds_end": null,
"cds_length": 762,
"cds_start": 125,
"consequences": [
"stop_gained"
],
"exon_count": 5,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "NM_001928.4",
"gene_hgnc_id": 2771,
"gene_symbol": "CFD",
"hgvs_c": "c.125C>A",
"hgvs_p": "p.Ser42*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000327726.11",
"protein_coding": true,
"protein_id": "NP_001919.2",
"strand": true,
"transcript": "NM_001928.4",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 253,
"aa_ref": "S",
"aa_start": 42,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 1191,
"cdna_start": 151,
"cds_end": null,
"cds_length": 762,
"cds_start": 125,
"consequences": [
"stop_gained"
],
"exon_count": 5,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000327726.11",
"gene_hgnc_id": 2771,
"gene_symbol": "CFD",
"hgvs_c": "c.125C>A",
"hgvs_p": "p.Ser42*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001928.4",
"protein_coding": true,
"protein_id": "ENSP00000332139.4",
"strand": true,
"transcript": "ENST00000327726.11",
"transcript_support_level": 1
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 260,
"aa_ref": "S",
"aa_start": 49,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1021,
"cdna_start": 172,
"cds_end": null,
"cds_length": 783,
"cds_start": 146,
"consequences": [
"stop_gained"
],
"exon_count": 5,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000592860.3",
"gene_hgnc_id": 2771,
"gene_symbol": "CFD",
"hgvs_c": "c.146C>A",
"hgvs_p": "p.Ser49*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000468253.1",
"strand": true,
"transcript": "ENST00000592860.3",
"transcript_support_level": 1
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 260,
"aa_ref": "S",
"aa_start": 49,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1212,
"cdna_start": 172,
"cds_end": null,
"cds_length": 783,
"cds_start": 146,
"consequences": [
"stop_gained"
],
"exon_count": 5,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "NM_001317335.2",
"gene_hgnc_id": 2771,
"gene_symbol": "CFD",
"hgvs_c": "c.146C>A",
"hgvs_p": "p.Ser49*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001304264.1",
"strand": true,
"transcript": "NM_001317335.2",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 253,
"aa_ref": "S",
"aa_start": 42,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1719,
"cdna_start": 151,
"cds_end": null,
"cds_length": 762,
"cds_start": 125,
"consequences": [
"stop_gained"
],
"exon_count": 6,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000866187.1",
"gene_hgnc_id": 2771,
"gene_symbol": "CFD",
"hgvs_c": "c.125C>A",
"hgvs_p": "p.Ser42*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000536246.1",
"strand": true,
"transcript": "ENST00000866187.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 250,
"aa_ref": "S",
"aa_start": 42,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 988,
"cdna_start": 149,
"cds_end": null,
"cds_length": 753,
"cds_start": 125,
"consequences": [
"stop_gained"
],
"exon_count": 5,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000965842.1",
"gene_hgnc_id": 2771,
"gene_symbol": "CFD",
"hgvs_c": "c.125C>A",
"hgvs_p": "p.Ser42*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000635901.1",
"strand": true,
"transcript": "ENST00000965842.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 236,
"aa_ref": "S",
"aa_start": 42,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 948,
"cdna_start": 151,
"cds_end": null,
"cds_length": 711,
"cds_start": 125,
"consequences": [
"stop_gained"
],
"exon_count": 5,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000695945.1",
"gene_hgnc_id": 2771,
"gene_symbol": "CFD",
"hgvs_c": "c.125C>A",
"hgvs_p": "p.Ser42*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000512278.1",
"strand": true,
"transcript": "ENST00000695945.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 214,
"aa_ref": "S",
"aa_start": 3,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 999,
"cdna_start": 150,
"cds_end": null,
"cds_length": 645,
"cds_start": 8,
"consequences": [
"stop_gained"
],
"exon_count": 5,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000695942.1",
"gene_hgnc_id": 2771,
"gene_symbol": "CFD",
"hgvs_c": "c.8C>A",
"hgvs_p": "p.Ser3*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000512275.1",
"strand": true,
"transcript": "ENST00000695942.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 214,
"aa_ref": "S",
"aa_start": 3,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 983,
"cdna_start": 134,
"cds_end": null,
"cds_length": 645,
"cds_start": 8,
"consequences": [
"stop_gained"
],
"exon_count": 5,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000695943.1",
"gene_hgnc_id": 2771,
"gene_symbol": "CFD",
"hgvs_c": "c.8C>A",
"hgvs_p": "p.Ser3*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000512276.1",
"strand": true,
"transcript": "ENST00000695943.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 214,
"aa_ref": "S",
"aa_start": 3,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1089,
"cdna_start": 242,
"cds_end": null,
"cds_length": 645,
"cds_start": 8,
"consequences": [
"stop_gained"
],
"exon_count": 5,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000695944.1",
"gene_hgnc_id": 2771,
"gene_symbol": "CFD",
"hgvs_c": "c.8C>A",
"hgvs_p": "p.Ser3*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000512277.1",
"strand": true,
"transcript": "ENST00000695944.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs104894667",
"effect": "stop_gained",
"frequency_reference_population": 0.000016851624,
"gene_hgnc_id": 2771,
"gene_symbol": "CFD",
"gnomad_exomes_ac": 23,
"gnomad_exomes_af": 0.0000165362,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 3,
"gnomad_genomes_af": 0.0000197376,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Pathogenic",
"phenotype_combined": "Recurrent Neisseria infections due to factor D deficiency|not provided",
"phylop100way_prediction": "Benign",
"phylop100way_score": 0.996,
"pos": 860686,
"ref": "C",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.15000000596046448,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.15,
"transcript": "NM_001317335.2"
}
]
}