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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: 2-98389696-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=98389696&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM1",
"PM2",
"PM5",
"PP2",
"PP3_Strong",
"PP5"
],
"effects": [
"missense_variant"
],
"gene_symbol": "CNGA3",
"hgnc_id": 2150,
"hgvs_c": "c.488C>A",
"hgvs_p": "p.Pro163Gln",
"inheritance_mode": "AR,AD",
"pathogenic_score": 12,
"score": 12,
"transcript": "NM_001298.3",
"verdict": "Pathogenic"
}
],
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM1,PM2,PM5,PP2,PP3_Strong,PP5",
"acmg_score": 12,
"allele_count_reference_population": 1,
"alphamissense_prediction": null,
"alphamissense_score": 0.5433,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.51,
"chr": "2",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_disease": "Inborn genetic diseases,not provided",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "LP:1 US:1",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.9537132978439331,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 694,
"aa_ref": "P",
"aa_start": 163,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3547,
"cdna_start": 604,
"cds_end": null,
"cds_length": 2085,
"cds_start": 488,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "NM_001298.3",
"gene_hgnc_id": 2150,
"gene_symbol": "CNGA3",
"hgvs_c": "c.488C>A",
"hgvs_p": "p.Pro163Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000272602.7",
"protein_coding": true,
"protein_id": "NP_001289.1",
"strand": true,
"transcript": "NM_001298.3",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 694,
"aa_ref": "P",
"aa_start": 163,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 3547,
"cdna_start": 604,
"cds_end": null,
"cds_length": 2085,
"cds_start": 488,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000272602.7",
"gene_hgnc_id": 2150,
"gene_symbol": "CNGA3",
"hgvs_c": "c.488C>A",
"hgvs_p": "p.Pro163Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001298.3",
"protein_coding": true,
"protein_id": "ENSP00000272602.2",
"strand": true,
"transcript": "ENST00000272602.7",
"transcript_support_level": 1
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 676,
"aa_ref": "P",
"aa_start": 145,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2504,
"cdna_start": 818,
"cds_end": null,
"cds_length": 2031,
"cds_start": 434,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000436404.6",
"gene_hgnc_id": 2150,
"gene_symbol": "CNGA3",
"hgvs_c": "c.434C>A",
"hgvs_p": "p.Pro145Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000410070.2",
"strand": true,
"transcript": "ENST00000436404.6",
"transcript_support_level": 1
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 749,
"aa_ref": "P",
"aa_start": 218,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4529,
"cdna_start": 1020,
"cds_end": null,
"cds_length": 2250,
"cds_start": 653,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000853268.1",
"gene_hgnc_id": 2150,
"gene_symbol": "CNGA3",
"hgvs_c": "c.653C>A",
"hgvs_p": "p.Pro218Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000523327.1",
"strand": true,
"transcript": "ENST00000853268.1",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 731,
"aa_ref": "P",
"aa_start": 200,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5046,
"cdna_start": 907,
"cds_end": null,
"cds_length": 2196,
"cds_start": 599,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000853267.1",
"gene_hgnc_id": 2150,
"gene_symbol": "CNGA3",
"hgvs_c": "c.599C>A",
"hgvs_p": "p.Pro200Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000523326.1",
"strand": true,
"transcript": "ENST00000853267.1",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 676,
"aa_ref": "P",
"aa_start": 145,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3493,
"cdna_start": 550,
"cds_end": null,
"cds_length": 2031,
"cds_start": 434,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "NM_001079878.2",
"gene_hgnc_id": 2150,
"gene_symbol": "CNGA3",
"hgvs_c": "c.434C>A",
"hgvs_p": "p.Pro145Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001073347.1",
"strand": true,
"transcript": "NM_001079878.2",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 638,
"aa_ref": "P",
"aa_start": 107,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4006,
"cdna_start": 497,
"cds_end": null,
"cds_length": 1917,
"cds_start": 320,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000853269.1",
"gene_hgnc_id": 2150,
"gene_symbol": "CNGA3",
"hgvs_c": "c.320C>A",
"hgvs_p": "p.Pro107Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000523328.1",
"strand": true,
"transcript": "ENST00000853269.1",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 749,
"aa_ref": "P",
"aa_start": 218,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3795,
"cdna_start": 852,
"cds_end": null,
"cds_length": 2250,
"cds_start": 653,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "XM_011510554.3",
"gene_hgnc_id": 2150,
"gene_symbol": "CNGA3",
"hgvs_c": "c.653C>A",
"hgvs_p": "p.Pro218Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011508856.1",
"strand": true,
"transcript": "XM_011510554.3",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 749,
"aa_ref": "P",
"aa_start": 218,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3712,
"cdna_start": 769,
"cds_end": null,
"cds_length": 2250,
"cds_start": 653,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "XM_047443222.1",
"gene_hgnc_id": 2150,
"gene_symbol": "CNGA3",
"hgvs_c": "c.653C>A",
"hgvs_p": "p.Pro218Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047299178.1",
"strand": true,
"transcript": "XM_047443222.1",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 731,
"aa_ref": "P",
"aa_start": 200,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3658,
"cdna_start": 715,
"cds_end": null,
"cds_length": 2196,
"cds_start": 599,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "XM_006712243.3",
"gene_hgnc_id": 2150,
"gene_symbol": "CNGA3",
"hgvs_c": "c.599C>A",
"hgvs_p": "p.Pro200Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_006712306.1",
"strand": true,
"transcript": "XM_006712243.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 569,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000393503.2",
"gene_hgnc_id": 2150,
"gene_symbol": "CNGA3",
"hgvs_c": "n.493C>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000393503.2",
"transcript_support_level": 4
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 2615,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 8,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000409937.1",
"gene_hgnc_id": 2150,
"gene_symbol": "CNGA3",
"hgvs_c": "n.641C>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000409937.1",
"transcript_support_level": 2
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs104893612",
"effect": "missense_variant",
"frequency_reference_population": 6.842341e-7,
"gene_hgnc_id": 2150,
"gene_symbol": "CNGA3",
"gnomad_exomes_ac": 1,
"gnomad_exomes_af": 6.84234e-7,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"phenotype_combined": "Inborn genetic diseases|not provided",
"phylop100way_prediction": "Pathogenic",
"phylop100way_score": 7.53,
"pos": 98389696,
"ref": "C",
"revel_prediction": "Pathogenic",
"revel_score": 0.951,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_001298.3"
}
]
}