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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: 1-40301183-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=40301183&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 40301183,
"ref": "C",
"alt": "T",
"effect": "stop_retained_variant",
"transcript": "NM_001852.4",
"consequences": [
{
"aa_ref": "*",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_retained_variant"
],
"exon_rank": 32,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL9A2",
"gene_hgnc_id": 2218,
"hgvs_c": "c.2069G>A",
"hgvs_p": "p.Ter690Ter",
"transcript": "NM_001852.4",
"protein_id": "NP_001843.1",
"transcript_support_level": null,
"aa_start": 690,
"aa_end": null,
"aa_length": 689,
"cds_start": 2069,
"cds_end": null,
"cds_length": 2070,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000372748.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001852.4"
},
{
"aa_ref": "*",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_retained_variant"
],
"exon_rank": 32,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL9A2",
"gene_hgnc_id": 2218,
"hgvs_c": "c.2069G>A",
"hgvs_p": "p.Ter690Ter",
"transcript": "ENST00000372748.8",
"protein_id": "ENSP00000361834.3",
"transcript_support_level": 1,
"aa_start": 690,
"aa_end": null,
"aa_length": 689,
"cds_start": 2069,
"cds_end": null,
"cds_length": 2070,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001852.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000372748.8"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 31,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL9A2",
"gene_hgnc_id": 2218,
"hgvs_c": "n.2372G>A",
"hgvs_p": null,
"transcript": "ENST00000482722.5",
"protein_id": null,
"transcript_support_level": 1,
"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": "retained_intron",
"feature": "ENST00000482722.5"
},
{
"aa_ref": "*",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_retained_variant"
],
"exon_rank": 32,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL9A2",
"gene_hgnc_id": 2218,
"hgvs_c": "c.2153G>A",
"hgvs_p": "p.Ter718Ter",
"transcript": "ENST00000869268.1",
"protein_id": "ENSP00000539327.1",
"transcript_support_level": null,
"aa_start": 718,
"aa_end": null,
"aa_length": 717,
"cds_start": 2153,
"cds_end": null,
"cds_length": 2154,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000869268.1"
},
{
"aa_ref": "*",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_retained_variant"
],
"exon_rank": 33,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL9A2",
"gene_hgnc_id": 2218,
"hgvs_c": "c.2081G>A",
"hgvs_p": "p.Ter694Ter",
"transcript": "ENST00000869264.1",
"protein_id": "ENSP00000539323.1",
"transcript_support_level": null,
"aa_start": 694,
"aa_end": null,
"aa_length": 693,
"cds_start": 2081,
"cds_end": null,
"cds_length": 2082,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000869264.1"
},
{
"aa_ref": "*",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_retained_variant"
],
"exon_rank": 32,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL9A2",
"gene_hgnc_id": 2218,
"hgvs_c": "c.2048G>A",
"hgvs_p": "p.Ter683Ter",
"transcript": "ENST00000869265.1",
"protein_id": "ENSP00000539324.1",
"transcript_support_level": null,
"aa_start": 683,
"aa_end": null,
"aa_length": 682,
"cds_start": 2048,
"cds_end": null,
"cds_length": 2049,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000869265.1"
},
{
"aa_ref": "*",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_retained_variant"
],
"exon_rank": 31,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL9A2",
"gene_hgnc_id": 2218,
"hgvs_c": "c.2015G>A",
"hgvs_p": "p.Ter672Ter",
"transcript": "ENST00000869266.1",
"protein_id": "ENSP00000539325.1",
"transcript_support_level": null,
"aa_start": 672,
"aa_end": null,
"aa_length": 671,
"cds_start": 2015,
"cds_end": null,
"cds_length": 2016,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000869266.1"
},
{
"aa_ref": "*",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_retained_variant"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL9A2",
"gene_hgnc_id": 2218,
"hgvs_c": "c.1916G>A",
"hgvs_p": "p.Ter639Ter",
"transcript": "ENST00000869267.1",
"protein_id": "ENSP00000539326.1",
"transcript_support_level": null,
"aa_start": 639,
"aa_end": null,
"aa_length": 638,
"cds_start": 1916,
"cds_end": null,
"cds_length": 1917,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000869267.1"
},
{
"aa_ref": "*",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_retained_variant"
],
"exon_rank": 32,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL9A2",
"gene_hgnc_id": 2218,
"hgvs_c": "c.2081G>A",
"hgvs_p": "p.Ter694Ter",
"transcript": "XM_017000332.2",
"protein_id": "XP_016855821.1",
"transcript_support_level": null,
"aa_start": 694,
"aa_end": null,
"aa_length": 693,
"cds_start": 2081,
"cds_end": null,
"cds_length": 2082,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017000332.2"
},
{
"aa_ref": "*",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_retained_variant"
],
"exon_rank": 32,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL9A2",
"gene_hgnc_id": 2218,
"hgvs_c": "c.1799G>A",
"hgvs_p": "p.Ter600Ter",
"transcript": "XM_011540715.3",
"protein_id": "XP_011539017.1",
"transcript_support_level": null,
"aa_start": 600,
"aa_end": null,
"aa_length": 599,
"cds_start": 1799,
"cds_end": null,
"cds_length": 1800,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011540715.3"
},
{
"aa_ref": "*",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_retained_variant"
],
"exon_rank": 31,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL9A2",
"gene_hgnc_id": 2218,
"hgvs_c": "c.1799G>A",
"hgvs_p": "p.Ter600Ter",
"transcript": "XM_011540716.3",
"protein_id": "XP_011539018.1",
"transcript_support_level": null,
"aa_start": 600,
"aa_end": null,
"aa_length": 599,
"cds_start": 1799,
"cds_end": null,
"cds_length": 1800,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011540716.3"
},
{
"aa_ref": "*",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_retained_variant"
],
"exon_rank": 31,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL9A2",
"gene_hgnc_id": 2218,
"hgvs_c": "c.1787G>A",
"hgvs_p": "p.Ter596Ter",
"transcript": "XM_017000333.2",
"protein_id": "XP_016855822.1",
"transcript_support_level": null,
"aa_start": 596,
"aa_end": null,
"aa_length": 595,
"cds_start": 1787,
"cds_end": null,
"cds_length": 1788,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017000333.2"
}
],
"gene_symbol": "COL9A2",
"gene_hgnc_id": 2218,
"dbsnp": "rs1239526286",
"frequency_reference_population": 0.000005476204,
"hom_count_reference_population": 0,
"allele_count_reference_population": 8,
"gnomad_exomes_af": 0.0000054762,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 8,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.36000001430511475,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.36,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.941,
"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": -5,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate,BP6_Moderate,BP7",
"acmg_by_gene": [
{
"score": -5,
"benign_score": 5,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6_Moderate",
"BP7"
],
"verdict": "Likely_benign",
"transcript": "NM_001852.4",
"gene_symbol": "COL9A2",
"hgnc_id": 2218,
"effects": [
"stop_retained_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.2069G>A",
"hgvs_p": "p.Ter690Ter"
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}