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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: 6-116462362-A-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=116462362&ref=A&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "6",
"pos": 116462362,
"ref": "A",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_001010919.3",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CALHM6",
"gene_hgnc_id": 33391,
"hgvs_c": "c.433A>C",
"hgvs_p": "p.Ser145Arg",
"transcript": "NM_001010919.3",
"protein_id": "NP_001010919.1",
"transcript_support_level": null,
"aa_start": 145,
"aa_end": null,
"aa_length": 315,
"cds_start": 433,
"cds_end": null,
"cds_length": 948,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000368605.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001010919.3"
},
{
"aa_ref": "S",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CALHM6",
"gene_hgnc_id": 33391,
"hgvs_c": "c.433A>C",
"hgvs_p": "p.Ser145Arg",
"transcript": "ENST00000368605.3",
"protein_id": "ENSP00000357594.1",
"transcript_support_level": 5,
"aa_start": 145,
"aa_end": null,
"aa_length": 315,
"cds_start": 433,
"cds_end": null,
"cds_length": 948,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001010919.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000368605.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "ENSG00000285446",
"gene_hgnc_id": null,
"hgvs_c": "c.767-921A>C",
"hgvs_p": null,
"transcript": "ENST00000644499.1",
"protein_id": "ENSP00000495266.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 282,
"cds_start": null,
"cds_end": null,
"cds_length": 849,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000644499.1"
},
{
"aa_ref": "S",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CALHM6",
"gene_hgnc_id": 33391,
"hgvs_c": "c.433A>C",
"hgvs_p": "p.Ser145Arg",
"transcript": "ENST00000859968.1",
"protein_id": "ENSP00000530027.1",
"transcript_support_level": null,
"aa_start": 145,
"aa_end": null,
"aa_length": 315,
"cds_start": 433,
"cds_end": null,
"cds_length": 948,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000859968.1"
},
{
"aa_ref": "S",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CALHM6",
"gene_hgnc_id": 33391,
"hgvs_c": "c.433A>C",
"hgvs_p": "p.Ser145Arg",
"transcript": "XM_011535845.4",
"protein_id": "XP_011534147.1",
"transcript_support_level": null,
"aa_start": 145,
"aa_end": null,
"aa_length": 337,
"cds_start": 433,
"cds_end": null,
"cds_length": 1014,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011535845.4"
},
{
"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": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "CALHM6",
"gene_hgnc_id": 33391,
"hgvs_c": "c.10-921A>C",
"hgvs_p": null,
"transcript": "NM_001276460.2",
"protein_id": "NP_001263389.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 143,
"cds_start": null,
"cds_end": null,
"cds_length": 432,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001276460.2"
},
{
"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": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "CALHM6",
"gene_hgnc_id": 33391,
"hgvs_c": "c.10-921A>C",
"hgvs_p": null,
"transcript": "ENST00000368606.8",
"protein_id": "ENSP00000357595.3",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 143,
"cds_start": null,
"cds_end": null,
"cds_length": 432,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000368606.8"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "CALHM6-AS1",
"gene_hgnc_id": 40971,
"hgvs_c": "n.75-1168T>G",
"hgvs_p": null,
"transcript": "ENST00000476099.1",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000476099.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "CALHM6-AS1",
"gene_hgnc_id": 40971,
"hgvs_c": "n.87-1168T>G",
"hgvs_p": null,
"transcript": "NR_174951.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_174951.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CALHM6",
"gene_hgnc_id": 33391,
"hgvs_c": "c.-105A>C",
"hgvs_p": null,
"transcript": "ENST00000368604.2",
"protein_id": "ENSP00000357593.2",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 158,
"cds_start": null,
"cds_end": null,
"cds_length": 477,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000368604.2"
}
],
"gene_symbol": "CALHM6",
"gene_hgnc_id": 33391,
"dbsnp": "rs992299039",
"frequency_reference_population": 0.00013770179,
"hom_count_reference_population": 0,
"allele_count_reference_population": 200,
"gnomad_exomes_af": 0.000143042,
"gnomad_genomes_af": 0.0000920471,
"gnomad_exomes_ac": 186,
"gnomad_genomes_ac": 14,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.10279372334480286,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.022,
"revel_prediction": "Benign",
"alphamissense_score": 0.1393,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.68,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -2.154,
"phylop100way_prediction": "Benign",
"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": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 2,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate"
],
"verdict": "Likely_benign",
"transcript": "NM_001010919.3",
"gene_symbol": "CALHM6",
"hgnc_id": 33391,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.433A>C",
"hgvs_p": "p.Ser145Arg"
},
{
"score": -2,
"benign_score": 2,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate"
],
"verdict": "Likely_benign",
"transcript": "ENST00000644499.1",
"gene_symbol": "ENSG00000285446",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.767-921A>C",
"hgvs_p": null
},
{
"score": -2,
"benign_score": 2,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate"
],
"verdict": "Likely_benign",
"transcript": "ENST00000476099.1",
"gene_symbol": "CALHM6-AS1",
"hgnc_id": 40971,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.75-1168T>G",
"hgvs_p": null
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}