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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: 1-234373513-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=234373513&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 20,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"effects": [
"missense_variant"
],
"gene_symbol": "COA6",
"hgnc_id": 18025,
"hgvs_c": "c.47G>C",
"hgvs_p": "p.Ser16Thr",
"inheritance_mode": "AR,Unknown",
"pathogenic_score": 0,
"score": -20,
"transcript": "NM_001206641.3",
"verdict": "Benign"
},
{
"benign_score": 20,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"effects": [
"splice_region_variant",
"intron_variant"
],
"gene_symbol": "COA6-AS1",
"hgnc_id": 40825,
"hgvs_c": "n.172+5C>G",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 0,
"score": -20,
"transcript": "ENST00000719174.1",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BA1",
"acmg_score": -20,
"allele_count_reference_population": 826173,
"alphamissense_prediction": "Benign",
"alphamissense_score": 0.1151,
"alt": "C",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.76,
"chr": "1",
"clinvar_classification": "Benign",
"clinvar_disease": " due to cytochrome c oxidase deficiency 4, fatal infantile,Cardioencephalomyopathy,not provided,not specified",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:3",
"computational_prediction_selected": "Benign",
"computational_score_selected": 8.487179457006278e-7,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 155,
"aa_ref": "S",
"aa_start": 16,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1741,
"cdna_start": 58,
"cds_end": null,
"cds_length": 468,
"cds_start": 47,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "NM_001206641.3",
"gene_hgnc_id": 18025,
"gene_symbol": "COA6",
"hgvs_c": "c.47G>C",
"hgvs_p": "p.Ser16Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000366615.10",
"protein_coding": true,
"protein_id": "NP_001193570.2",
"strand": true,
"transcript": "NM_001206641.3",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 155,
"aa_ref": "S",
"aa_start": 16,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 1741,
"cdna_start": 58,
"cds_end": null,
"cds_length": 468,
"cds_start": 47,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000366615.10",
"gene_hgnc_id": 18025,
"gene_symbol": "COA6",
"hgvs_c": "c.47G>C",
"hgvs_p": "p.Ser16Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001206641.3",
"protein_coding": true,
"protein_id": "ENSP00000355574.5",
"strand": true,
"transcript": "ENST00000366615.10",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 79,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 697,
"cdna_start": null,
"cds_end": null,
"cds_length": 240,
"cds_start": null,
"consequences": [
"5_prime_UTR_variant"
],
"exon_count": 3,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000619305.1",
"gene_hgnc_id": 18025,
"gene_symbol": "COA6",
"hgvs_c": "c.-182G>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000479686.1",
"strand": true,
"transcript": "ENST00000619305.1",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 671,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 2,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000451795.4",
"gene_hgnc_id": 40825,
"gene_symbol": "COA6-AS1",
"hgvs_c": "n.177C>G",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000451795.4",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 1056,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 1,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000685022.3",
"gene_hgnc_id": 40825,
"gene_symbol": "COA6-AS1",
"hgvs_c": "n.345C>G",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000685022.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 612,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 2,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000719173.1",
"gene_hgnc_id": 40825,
"gene_symbol": "COA6-AS1",
"hgvs_c": "n.141C>G",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000719173.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 575,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 2,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "NR_125961.1",
"gene_hgnc_id": 40825,
"gene_symbol": "COA6-AS1",
"hgvs_c": "n.81C>G",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "NR_125961.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 416,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000719174.1",
"gene_hgnc_id": 40825,
"gene_symbol": "COA6-AS1",
"hgvs_c": "n.172+5C>G",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000719174.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 125,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 641,
"cdna_start": null,
"cds_end": null,
"cds_length": 378,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000366613.1",
"gene_hgnc_id": 18025,
"gene_symbol": "COA6",
"hgvs_c": "c.-206G>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000355572.1",
"strand": true,
"transcript": "ENST00000366613.1",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 79,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1013,
"cdna_start": null,
"cds_end": null,
"cds_length": 240,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000366612.1",
"gene_hgnc_id": 18025,
"gene_symbol": "COA6",
"hgvs_c": "c.-733G>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000355571.1",
"strand": true,
"transcript": "ENST00000366612.1",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 125,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 645,
"cdna_start": null,
"cds_end": null,
"cds_length": 378,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_001012985.2",
"gene_hgnc_id": 18025,
"gene_symbol": "COA6",
"hgvs_c": "c.-206G>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001013003.1",
"strand": true,
"transcript": "NM_001012985.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 79,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1016,
"cdna_start": null,
"cds_end": null,
"cds_length": 240,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_001301733.1",
"gene_hgnc_id": 18025,
"gene_symbol": "COA6",
"hgvs_c": "c.-733G>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001288662.1",
"strand": true,
"transcript": "NM_001301733.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 281,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000719175.1",
"gene_hgnc_id": 40825,
"gene_symbol": "COA6-AS1",
"hgvs_c": "n.-94C>G",
"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": "ENST00000719175.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 597,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 1,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NR_125962.1",
"gene_hgnc_id": 40825,
"gene_symbol": "COA6-AS1",
"hgvs_c": "n.-110C>G",
"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": "NR_125962.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs10910420",
"effect": "missense_variant",
"frequency_reference_population": 0.5147784,
"gene_hgnc_id": 18025,
"gene_symbol": "COA6",
"gnomad_exomes_ac": 735150,
"gnomad_exomes_af": 0.506063,
"gnomad_exomes_homalt": 189330,
"gnomad_genomes_ac": 91023,
"gnomad_genomes_af": 0.597946,
"gnomad_genomes_homalt": 29116,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 218446,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Benign",
"phenotype_combined": "not specified|Cardioencephalomyopathy, fatal infantile, due to cytochrome c oxidase deficiency 4|not provided",
"phylop100way_prediction": "Benign",
"phylop100way_score": -3.427,
"pos": 234373513,
"ref": "G",
"revel_prediction": "Benign",
"revel_score": 0.041,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_001206641.3"
}
]
}