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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: 12-48917004-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=48917004&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 48917004,
"ref": "C",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000320516.5",
"consequences": [
{
"aa_ref": "H",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DRC2",
"gene_hgnc_id": 29937,
"hgvs_c": "c.505C>A",
"hgvs_p": "p.His169Asn",
"transcript": "NM_033124.5",
"protein_id": "NP_149115.2",
"transcript_support_level": null,
"aa_start": 169,
"aa_end": null,
"aa_length": 484,
"cds_start": 505,
"cds_end": null,
"cds_length": 1455,
"cdna_start": 709,
"cdna_end": null,
"cdna_length": 1792,
"mane_select": "ENST00000320516.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CCDC65",
"gene_hgnc_id": 29937,
"hgvs_c": "c.505C>A",
"hgvs_p": "p.His169Asn",
"transcript": "ENST00000320516.5",
"protein_id": "ENSP00000312706.4",
"transcript_support_level": 1,
"aa_start": 169,
"aa_end": null,
"aa_length": 484,
"cds_start": 505,
"cds_end": null,
"cds_length": 1455,
"cdna_start": 709,
"cdna_end": null,
"cdna_length": 1792,
"mane_select": "NM_033124.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "ENSG00000272822",
"gene_hgnc_id": null,
"hgvs_c": "c.385-13096G>T",
"hgvs_p": null,
"transcript": "ENST00000398092.4",
"protein_id": "ENSP00000438507.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 210,
"cds_start": -4,
"cds_end": null,
"cds_length": 633,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 939,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CCDC65",
"gene_hgnc_id": 29937,
"hgvs_c": "c.505C>A",
"hgvs_p": "p.His169Asn",
"transcript": "ENST00000266984.9",
"protein_id": "ENSP00000266984.5",
"transcript_support_level": 5,
"aa_start": 169,
"aa_end": null,
"aa_length": 497,
"cds_start": 505,
"cds_end": null,
"cds_length": 1494,
"cdna_start": 732,
"cdna_end": null,
"cdna_length": 2084,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DRC2",
"gene_hgnc_id": 29937,
"hgvs_c": "c.76C>A",
"hgvs_p": "p.His26Asn",
"transcript": "NM_001286957.2",
"protein_id": "NP_001273886.1",
"transcript_support_level": null,
"aa_start": 26,
"aa_end": null,
"aa_length": 341,
"cds_start": 76,
"cds_end": null,
"cds_length": 1026,
"cdna_start": 669,
"cdna_end": null,
"cdna_length": 1752,
"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": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CCDC65",
"gene_hgnc_id": 29937,
"hgvs_c": "n.*336C>A",
"hgvs_p": null,
"transcript": "ENST00000547861.5",
"protein_id": "ENSP00000447157.1",
"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": 1746,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CCDC65",
"gene_hgnc_id": 29937,
"hgvs_c": "n.*336C>A",
"hgvs_p": null,
"transcript": "ENST00000547861.5",
"protein_id": "ENSP00000447157.1",
"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": 1746,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "CCDC65",
"gene_hgnc_id": 29937,
"hgvs_c": "c.301-1271C>A",
"hgvs_p": null,
"transcript": "ENST00000552942.5",
"protein_id": "ENSP00000446569.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 372,
"cds_start": -4,
"cds_end": null,
"cds_length": 1120,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1338,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "CCDC65",
"gene_hgnc_id": 29937,
"dbsnp": "rs79716342",
"frequency_reference_population": 0.05114501,
"hom_count_reference_population": 2591,
"allele_count_reference_population": 82537,
"gnomad_exomes_af": 0.0520306,
"gnomad_genomes_af": 0.0426417,
"gnomad_exomes_ac": 76046,
"gnomad_genomes_ac": 6491,
"gnomad_exomes_homalt": 2387,
"gnomad_genomes_homalt": 204,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.001727461814880371,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.145,
"revel_prediction": "Benign",
"alphamissense_score": 0.097,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.75,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.12,
"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": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BA1",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000320516.5",
"gene_symbol": "CCDC65",
"hgnc_id": 29937,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.505C>A",
"hgvs_p": "p.His169Asn"
},
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000398092.4",
"gene_symbol": "ENSG00000272822",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.385-13096G>T",
"hgvs_p": null
},
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "NM_033124.5",
"gene_symbol": "DRC2",
"hgnc_id": 29937,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.505C>A",
"hgvs_p": "p.His169Asn"
}
],
"clinvar_disease": "Primary ciliary dyskinesia 27,not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:4",
"phenotype_combined": "not specified|Primary ciliary dyskinesia 27|not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}