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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: 1-42754924-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=42754924&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 42754924,
"ref": "G",
"alt": "C",
"effect": "synonymous_variant",
"transcript": "ENST00000296388.10",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "P3H1",
"gene_hgnc_id": 19316,
"hgvs_c": "c.1290C>G",
"hgvs_p": "p.Thr430Thr",
"transcript": "NM_022356.4",
"protein_id": "NP_071751.3",
"transcript_support_level": null,
"aa_start": 430,
"aa_end": null,
"aa_length": 736,
"cds_start": 1290,
"cds_end": null,
"cds_length": 2211,
"cdna_start": 1347,
"cdna_end": null,
"cdna_length": 2591,
"mane_select": "ENST00000296388.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "P3H1",
"gene_hgnc_id": 19316,
"hgvs_c": "c.1290C>G",
"hgvs_p": "p.Thr430Thr",
"transcript": "ENST00000296388.10",
"protein_id": "ENSP00000296388.5",
"transcript_support_level": 1,
"aa_start": 430,
"aa_end": null,
"aa_length": 736,
"cds_start": 1290,
"cds_end": null,
"cds_length": 2211,
"cdna_start": 1347,
"cdna_end": null,
"cdna_length": 2591,
"mane_select": "NM_022356.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "P3H1",
"gene_hgnc_id": 19316,
"hgvs_c": "c.1290C>G",
"hgvs_p": "p.Thr430Thr",
"transcript": "ENST00000397054.7",
"protein_id": "ENSP00000380245.3",
"transcript_support_level": 1,
"aa_start": 430,
"aa_end": null,
"aa_length": 697,
"cds_start": 1290,
"cds_end": null,
"cds_length": 2094,
"cdna_start": 1403,
"cdna_end": null,
"cdna_length": 2705,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "P3H1",
"gene_hgnc_id": 19316,
"hgvs_c": "c.1290C>G",
"hgvs_p": "p.Thr430Thr",
"transcript": "NM_001243246.2",
"protein_id": "NP_001230175.1",
"transcript_support_level": null,
"aa_start": 430,
"aa_end": null,
"aa_length": 804,
"cds_start": 1290,
"cds_end": null,
"cds_length": 2415,
"cdna_start": 1347,
"cdna_end": null,
"cdna_length": 3010,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "P3H1",
"gene_hgnc_id": 19316,
"hgvs_c": "c.1290C>G",
"hgvs_p": "p.Thr430Thr",
"transcript": "ENST00000236040.8",
"protein_id": "ENSP00000236040.4",
"transcript_support_level": 2,
"aa_start": 430,
"aa_end": null,
"aa_length": 804,
"cds_start": 1290,
"cds_end": null,
"cds_length": 2415,
"cdna_start": 1331,
"cdna_end": null,
"cdna_length": 2993,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "P3H1",
"gene_hgnc_id": 19316,
"hgvs_c": "c.1290C>G",
"hgvs_p": "p.Thr430Thr",
"transcript": "NM_001146289.2",
"protein_id": "NP_001139761.1",
"transcript_support_level": null,
"aa_start": 430,
"aa_end": null,
"aa_length": 697,
"cds_start": 1290,
"cds_end": null,
"cds_length": 2094,
"cdna_start": 1347,
"cdna_end": null,
"cdna_length": 2610,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "P3H1",
"gene_hgnc_id": 19316,
"hgvs_c": "c.1290C>G",
"hgvs_p": "p.Thr430Thr",
"transcript": "XM_047427616.1",
"protein_id": "XP_047283572.1",
"transcript_support_level": null,
"aa_start": 430,
"aa_end": null,
"aa_length": 803,
"cds_start": 1290,
"cds_end": null,
"cds_length": 2412,
"cdna_start": 1347,
"cdna_end": null,
"cdna_length": 2792,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "P3H1",
"gene_hgnc_id": 19316,
"hgvs_c": "c.315C>G",
"hgvs_p": "p.Thr105Thr",
"transcript": "XM_047427621.1",
"protein_id": "XP_047283577.1",
"transcript_support_level": null,
"aa_start": 105,
"aa_end": null,
"aa_length": 478,
"cds_start": 315,
"cds_end": null,
"cds_length": 1437,
"cdna_start": 399,
"cdna_end": null,
"cdna_length": 1844,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "P3H1",
"gene_hgnc_id": 19316,
"hgvs_c": "c.312C>G",
"hgvs_p": "p.Thr104Thr",
"transcript": "XM_047427626.1",
"protein_id": "XP_047283582.1",
"transcript_support_level": null,
"aa_start": 104,
"aa_end": null,
"aa_length": 477,
"cds_start": 312,
"cds_end": null,
"cds_length": 1434,
"cdna_start": 396,
"cdna_end": null,
"cdna_length": 1841,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "P3H1",
"gene_hgnc_id": 19316,
"hgvs_c": "c.183C>G",
"hgvs_p": "p.Thr61Thr",
"transcript": "XM_047427629.1",
"protein_id": "XP_047283585.1",
"transcript_support_level": null,
"aa_start": 61,
"aa_end": null,
"aa_length": 434,
"cds_start": 183,
"cds_end": null,
"cds_length": 1305,
"cdna_start": 278,
"cdna_end": null,
"cdna_length": 1723,
"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": 2,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "P3H1",
"gene_hgnc_id": 19316,
"hgvs_c": "n.111C>G",
"hgvs_p": null,
"transcript": "ENST00000431412.3",
"protein_id": "ENSP00000408056.1",
"transcript_support_level": 5,
"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": 836,
"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": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "P3H1",
"gene_hgnc_id": 19316,
"hgvs_c": "n.64C>G",
"hgvs_p": null,
"transcript": "ENST00000447502.2",
"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": 453,
"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": 7,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "P3H1",
"gene_hgnc_id": 19316,
"hgvs_c": "n.1482C>G",
"hgvs_p": null,
"transcript": "ENST00000460031.5",
"protein_id": null,
"transcript_support_level": 5,
"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": 2726,
"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": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "P3H1",
"gene_hgnc_id": 19316,
"hgvs_c": "n.13C>G",
"hgvs_p": null,
"transcript": "ENST00000481465.3",
"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": 728,
"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": 8,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "P3H1",
"gene_hgnc_id": 19316,
"hgvs_c": "n.1570C>G",
"hgvs_p": null,
"transcript": "ENST00000495874.5",
"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": 2813,
"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": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "P3H1",
"gene_hgnc_id": 19316,
"hgvs_c": "n.1415C>G",
"hgvs_p": null,
"transcript": "XR_946739.3",
"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": 1432,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "P3H1",
"gene_hgnc_id": 19316,
"hgvs_c": "n.*56C>G",
"hgvs_p": null,
"transcript": "ENST00000463465.1",
"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": 897,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "P3H1",
"gene_hgnc_id": 19316,
"dbsnp": "rs771496600",
"frequency_reference_population": 0.000008054373,
"hom_count_reference_population": 0,
"allele_count_reference_population": 13,
"gnomad_exomes_af": 0.00000752453,
"gnomad_genomes_af": 0.0000131454,
"gnomad_exomes_ac": 11,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.01899999938905239,
"computational_prediction_selected": "Benign",
"computational_source_selected": "REVEL",
"splice_score_selected": 0.029999999329447746,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.019,
"revel_prediction": "Benign",
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.5,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.643,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.03,
"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": "ENST00000296388.10",
"gene_symbol": "P3H1",
"hgnc_id": 19316,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.1290C>G",
"hgvs_p": "p.Thr430Thr"
}
],
"clinvar_disease": "Osteogenesis imperfecta type 8",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "Osteogenesis imperfecta type 8",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}