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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: 15-100569339-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=15&pos=100569339&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "15",
"pos": 100569339,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_001040616.3",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LINS1",
"gene_hgnc_id": 30922,
"hgvs_c": "c.2173C>T",
"hgvs_p": "p.Arg725Cys",
"transcript": "NM_001040616.3",
"protein_id": "NP_001035706.2",
"transcript_support_level": null,
"aa_start": 725,
"aa_end": null,
"aa_length": 757,
"cds_start": 2173,
"cds_end": null,
"cds_length": 2274,
"cdna_start": 2340,
"cdna_end": null,
"cdna_length": 4755,
"mane_select": "ENST00000314742.13",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LINS1",
"gene_hgnc_id": 30922,
"hgvs_c": "c.2173C>T",
"hgvs_p": "p.Arg725Cys",
"transcript": "ENST00000314742.13",
"protein_id": "ENSP00000318423.8",
"transcript_support_level": 5,
"aa_start": 725,
"aa_end": null,
"aa_length": 757,
"cds_start": 2173,
"cds_end": null,
"cds_length": 2274,
"cdna_start": 2340,
"cdna_end": null,
"cdna_length": 4755,
"mane_select": "NM_001040616.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LINS1",
"gene_hgnc_id": 30922,
"hgvs_c": "c.2020C>T",
"hgvs_p": "p.Arg674Cys",
"transcript": "NM_001352508.2",
"protein_id": "NP_001339437.1",
"transcript_support_level": null,
"aa_start": 674,
"aa_end": null,
"aa_length": 706,
"cds_start": 2020,
"cds_end": null,
"cds_length": 2121,
"cdna_start": 2187,
"cdna_end": null,
"cdna_length": 4602,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LINS1",
"gene_hgnc_id": 30922,
"hgvs_c": "c.1426C>T",
"hgvs_p": "p.Arg476Cys",
"transcript": "NM_001352507.2",
"protein_id": "NP_001339436.1",
"transcript_support_level": null,
"aa_start": 476,
"aa_end": null,
"aa_length": 508,
"cds_start": 1426,
"cds_end": null,
"cds_length": 1527,
"cdna_start": 2502,
"cdna_end": null,
"cdna_length": 4917,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LINS1",
"gene_hgnc_id": 30922,
"hgvs_c": "c.2173C>T",
"hgvs_p": "p.Arg725Cys",
"transcript": "XM_005254941.3",
"protein_id": "XP_005254998.1",
"transcript_support_level": null,
"aa_start": 725,
"aa_end": null,
"aa_length": 757,
"cds_start": 2173,
"cds_end": null,
"cds_length": 2274,
"cdna_start": 2344,
"cdna_end": null,
"cdna_length": 4759,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LINS1",
"gene_hgnc_id": 30922,
"hgvs_c": "c.2173C>T",
"hgvs_p": "p.Arg725Cys",
"transcript": "XM_024449980.2",
"protein_id": "XP_024305748.1",
"transcript_support_level": null,
"aa_start": 725,
"aa_end": null,
"aa_length": 757,
"cds_start": 2173,
"cds_end": null,
"cds_length": 2274,
"cdna_start": 3229,
"cdna_end": null,
"cdna_length": 5644,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LINS1",
"gene_hgnc_id": 30922,
"hgvs_c": "c.2065C>T",
"hgvs_p": "p.Arg689Cys",
"transcript": "XM_005254943.3",
"protein_id": "XP_005255000.1",
"transcript_support_level": null,
"aa_start": 689,
"aa_end": null,
"aa_length": 721,
"cds_start": 2065,
"cds_end": null,
"cds_length": 2166,
"cdna_start": 2232,
"cdna_end": null,
"cdna_length": 4647,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LINS1",
"gene_hgnc_id": 30922,
"hgvs_c": "c.2065C>T",
"hgvs_p": "p.Arg689Cys",
"transcript": "XM_047432784.1",
"protein_id": "XP_047288740.1",
"transcript_support_level": null,
"aa_start": 689,
"aa_end": null,
"aa_length": 721,
"cds_start": 2065,
"cds_end": null,
"cds_length": 2166,
"cdna_start": 2236,
"cdna_end": null,
"cdna_length": 4651,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LINS1",
"gene_hgnc_id": 30922,
"hgvs_c": "c.2065C>T",
"hgvs_p": "p.Arg689Cys",
"transcript": "XM_047432785.1",
"protein_id": "XP_047288741.1",
"transcript_support_level": null,
"aa_start": 689,
"aa_end": null,
"aa_length": 721,
"cds_start": 2065,
"cds_end": null,
"cds_length": 2166,
"cdna_start": 3121,
"cdna_end": null,
"cdna_length": 5536,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LINS1",
"gene_hgnc_id": 30922,
"hgvs_c": "c.1426C>T",
"hgvs_p": "p.Arg476Cys",
"transcript": "XM_017022399.3",
"protein_id": "XP_016877888.1",
"transcript_support_level": null,
"aa_start": 476,
"aa_end": null,
"aa_length": 508,
"cds_start": 1426,
"cds_end": null,
"cds_length": 1527,
"cdna_start": 1706,
"cdna_end": null,
"cdna_length": 4121,
"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": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LINS1",
"gene_hgnc_id": 30922,
"hgvs_c": "n.2448C>T",
"hgvs_p": null,
"transcript": "ENST00000559169.1",
"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": 2552,
"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": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LINS1",
"gene_hgnc_id": 30922,
"hgvs_c": "n.2296C>T",
"hgvs_p": null,
"transcript": "NR_148017.2",
"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": 4711,
"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": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LINS1",
"gene_hgnc_id": 30922,
"hgvs_c": "n.2284C>T",
"hgvs_p": null,
"transcript": "NR_148018.2",
"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": 4699,
"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": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LINS1",
"gene_hgnc_id": 30922,
"hgvs_c": "n.3579C>T",
"hgvs_p": null,
"transcript": "NR_148019.2",
"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": 5994,
"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": "LINS1",
"gene_hgnc_id": 30922,
"hgvs_c": "n.2442C>T",
"hgvs_p": null,
"transcript": "XR_007064471.1",
"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": 4857,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "LINS1",
"gene_hgnc_id": 30922,
"hgvs_c": "n.191-4074C>T",
"hgvs_p": null,
"transcript": "ENST00000560783.1",
"protein_id": "ENSP00000474128.1",
"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": 511,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "LINS1",
"gene_hgnc_id": 30922,
"dbsnp": "rs371728866",
"frequency_reference_population": 0.00000743534,
"hom_count_reference_population": 0,
"allele_count_reference_population": 12,
"gnomad_exomes_af": 0.00000615693,
"gnomad_genomes_af": 0.0000197179,
"gnomad_exomes_ac": 9,
"gnomad_genomes_ac": 3,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8027282953262329,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.263,
"revel_prediction": "Benign",
"alphamissense_score": 0.3506,
"alphamissense_prediction": "Uncertain_significance",
"bayesdelnoaf_score": 0.09,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 5.227,
"phylop100way_prediction": "Uncertain_significance",
"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": 3,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3",
"acmg_by_gene": [
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PM2",
"PP3"
],
"verdict": "Uncertain_significance",
"transcript": "NM_001040616.3",
"gene_symbol": "LINS1",
"hgnc_id": 30922,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2173C>T",
"hgvs_p": "p.Arg725Cys"
}
],
"clinvar_disease": "Inborn genetic diseases",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Inborn genetic diseases",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}