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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: 2-98396839-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=98396839&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 98396839,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000272602.7",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CNGA3",
"gene_hgnc_id": 2150,
"hgvs_c": "c.1669G>A",
"hgvs_p": "p.Gly557Arg",
"transcript": "NM_001298.3",
"protein_id": "NP_001289.1",
"transcript_support_level": null,
"aa_start": 557,
"aa_end": null,
"aa_length": 694,
"cds_start": 1669,
"cds_end": null,
"cds_length": 2085,
"cdna_start": 1785,
"cdna_end": null,
"cdna_length": 3547,
"mane_select": "ENST00000272602.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CNGA3",
"gene_hgnc_id": 2150,
"hgvs_c": "c.1669G>A",
"hgvs_p": "p.Gly557Arg",
"transcript": "ENST00000272602.7",
"protein_id": "ENSP00000272602.2",
"transcript_support_level": 1,
"aa_start": 557,
"aa_end": null,
"aa_length": 694,
"cds_start": 1669,
"cds_end": null,
"cds_length": 2085,
"cdna_start": 1785,
"cdna_end": null,
"cdna_length": 3547,
"mane_select": "NM_001298.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CNGA3",
"gene_hgnc_id": 2150,
"hgvs_c": "c.1615G>A",
"hgvs_p": "p.Gly539Arg",
"transcript": "ENST00000436404.6",
"protein_id": "ENSP00000410070.2",
"transcript_support_level": 1,
"aa_start": 539,
"aa_end": null,
"aa_length": 676,
"cds_start": 1615,
"cds_end": null,
"cds_length": 2031,
"cdna_start": 1999,
"cdna_end": null,
"cdna_length": 2504,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CNGA3",
"gene_hgnc_id": 2150,
"hgvs_c": "c.1615G>A",
"hgvs_p": "p.Gly539Arg",
"transcript": "NM_001079878.2",
"protein_id": "NP_001073347.1",
"transcript_support_level": null,
"aa_start": 539,
"aa_end": null,
"aa_length": 676,
"cds_start": 1615,
"cds_end": null,
"cds_length": 2031,
"cdna_start": 1731,
"cdna_end": null,
"cdna_length": 3493,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CNGA3",
"gene_hgnc_id": 2150,
"hgvs_c": "c.1834G>A",
"hgvs_p": "p.Gly612Arg",
"transcript": "XM_011510554.3",
"protein_id": "XP_011508856.1",
"transcript_support_level": null,
"aa_start": 612,
"aa_end": null,
"aa_length": 749,
"cds_start": 1834,
"cds_end": null,
"cds_length": 2250,
"cdna_start": 2033,
"cdna_end": null,
"cdna_length": 3795,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CNGA3",
"gene_hgnc_id": 2150,
"hgvs_c": "c.1834G>A",
"hgvs_p": "p.Gly612Arg",
"transcript": "XM_047443222.1",
"protein_id": "XP_047299178.1",
"transcript_support_level": null,
"aa_start": 612,
"aa_end": null,
"aa_length": 749,
"cds_start": 1834,
"cds_end": null,
"cds_length": 2250,
"cdna_start": 1950,
"cdna_end": null,
"cdna_length": 3712,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CNGA3",
"gene_hgnc_id": 2150,
"hgvs_c": "c.1780G>A",
"hgvs_p": "p.Gly594Arg",
"transcript": "XM_006712243.3",
"protein_id": "XP_006712306.1",
"transcript_support_level": null,
"aa_start": 594,
"aa_end": null,
"aa_length": 731,
"cds_start": 1780,
"cds_end": null,
"cds_length": 2196,
"cdna_start": 1896,
"cdna_end": null,
"cdna_length": 3658,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CNGA3",
"gene_hgnc_id": 2150,
"hgvs_c": "n.1822G>A",
"hgvs_p": null,
"transcript": "ENST00000409937.1",
"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": 2615,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "CNGA3",
"gene_hgnc_id": 2150,
"dbsnp": "rs104893615",
"frequency_reference_population": 0.00007868337,
"hom_count_reference_population": 0,
"allele_count_reference_population": 127,
"gnomad_exomes_af": 0.0000752454,
"gnomad_genomes_af": 0.00011171,
"gnomad_exomes_ac": 110,
"gnomad_genomes_ac": 17,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.6520953178405762,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.965,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9848,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.58,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 9.602,
"phylop100way_prediction": "Pathogenic",
"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": 11,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM1,PP2,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 11,
"benign_score": 0,
"pathogenic_score": 11,
"criteria": [
"PM1",
"PP2",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000272602.7",
"gene_symbol": "CNGA3",
"hgnc_id": 2150,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.1669G>A",
"hgvs_p": "p.Gly557Arg"
}
],
"clinvar_disease": "Achromatopsia,Achromatopsia 2,Inborn genetic diseases,Retinal dystrophy,not provided,not specified",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:3 LP:3 US:1",
"phenotype_combined": "Achromatopsia 2|not provided|Achromatopsia|not specified|Retinal dystrophy|Inborn genetic diseases",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}