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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: 1-203225706-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=203225706&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 203225706,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000367229.6",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHIT1",
"gene_hgnc_id": 1936,
"hgvs_c": "c.220G>A",
"hgvs_p": "p.Glu74Lys",
"transcript": "NM_003465.3",
"protein_id": "NP_003456.1",
"transcript_support_level": null,
"aa_start": 74,
"aa_end": null,
"aa_length": 466,
"cds_start": 220,
"cds_end": null,
"cds_length": 1401,
"cdna_start": 257,
"cdna_end": null,
"cdna_length": 2248,
"mane_select": "ENST00000367229.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHIT1",
"gene_hgnc_id": 1936,
"hgvs_c": "c.220G>A",
"hgvs_p": "p.Glu74Lys",
"transcript": "ENST00000367229.6",
"protein_id": "ENSP00000356198.1",
"transcript_support_level": 1,
"aa_start": 74,
"aa_end": null,
"aa_length": 466,
"cds_start": 220,
"cds_end": null,
"cds_length": 1401,
"cdna_start": 257,
"cdna_end": null,
"cdna_length": 2248,
"mane_select": "NM_003465.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHIT1",
"gene_hgnc_id": 1936,
"hgvs_c": "n.220G>A",
"hgvs_p": null,
"transcript": "ENST00000491855.5",
"protein_id": "ENSP00000423778.1",
"transcript_support_level": 1,
"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": 1700,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHIT1",
"gene_hgnc_id": 1936,
"hgvs_c": "n.220G>A",
"hgvs_p": null,
"transcript": "ENST00000503786.1",
"protein_id": "ENSP00000421617.1",
"transcript_support_level": 1,
"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": 1605,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHIT1",
"gene_hgnc_id": 1936,
"hgvs_c": "c.220G>A",
"hgvs_p": "p.Glu74Lys",
"transcript": "NM_001256125.2",
"protein_id": "NP_001243054.2",
"transcript_support_level": null,
"aa_start": 74,
"aa_end": null,
"aa_length": 447,
"cds_start": 220,
"cds_end": null,
"cds_length": 1344,
"cdna_start": 257,
"cdna_end": null,
"cdna_length": 2191,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHIT1",
"gene_hgnc_id": 1936,
"hgvs_c": "c.220G>A",
"hgvs_p": "p.Glu74Lys",
"transcript": "ENST00000255427.7",
"protein_id": "ENSP00000255427.3",
"transcript_support_level": 2,
"aa_start": 74,
"aa_end": null,
"aa_length": 447,
"cds_start": 220,
"cds_end": null,
"cds_length": 1344,
"cdna_start": 255,
"cdna_end": null,
"cdna_length": 1598,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHIT1",
"gene_hgnc_id": 1936,
"hgvs_c": "c.265G>A",
"hgvs_p": "p.Glu89Lys",
"transcript": "XM_047442899.1",
"protein_id": "XP_047298855.1",
"transcript_support_level": null,
"aa_start": 89,
"aa_end": null,
"aa_length": 481,
"cds_start": 265,
"cds_end": null,
"cds_length": 1446,
"cdna_start": 280,
"cdna_end": null,
"cdna_length": 2271,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHIT1",
"gene_hgnc_id": 1936,
"hgvs_c": "n.4577G>A",
"hgvs_p": null,
"transcript": "ENST00000484834.5",
"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": 5607,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHIT1",
"gene_hgnc_id": 1936,
"hgvs_c": "n.416G>A",
"hgvs_p": null,
"transcript": "ENST00000513472.5",
"protein_id": null,
"transcript_support_level": 3,
"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": 583,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHIT1",
"gene_hgnc_id": 1936,
"hgvs_c": "n.257G>A",
"hgvs_p": null,
"transcript": "NR_045784.2",
"protein_id": null,
"transcript_support_level": null,
"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": 2476,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHIT1",
"gene_hgnc_id": 1936,
"hgvs_c": "n.257G>A",
"hgvs_p": null,
"transcript": "NR_045785.2",
"protein_id": null,
"transcript_support_level": null,
"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": 2319,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "CHIT1",
"gene_hgnc_id": 1936,
"dbsnp": "rs137852607",
"frequency_reference_population": 0.0044021173,
"hom_count_reference_population": 26,
"allele_count_reference_population": 7105,
"gnomad_exomes_af": 0.00450272,
"gnomad_genomes_af": 0.00343595,
"gnomad_exomes_ac": 6582,
"gnomad_genomes_ac": 523,
"gnomad_exomes_homalt": 24,
"gnomad_genomes_homalt": 2,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.04031744599342346,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.282,
"revel_prediction": "Benign",
"alphamissense_score": 0.0717,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.41,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.709,
"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": -9,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6,BS2",
"acmg_by_gene": [
{
"score": -9,
"benign_score": 9,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000367229.6",
"gene_symbol": "CHIT1",
"hgnc_id": 1936,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.220G>A",
"hgvs_p": "p.Glu74Lys"
}
],
"clinvar_disease": "Chitotriosidase deficiency",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 B:1",
"phenotype_combined": "Chitotriosidase deficiency",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}