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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: 5-36984980-TA-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=36984980&ref=TA&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 36984980,
"ref": "TA",
"alt": "T",
"effect": "frameshift_variant",
"transcript": "ENST00000282516.13",
"consequences": [
{
"aa_ref": "K",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 47,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NIPBL",
"gene_hgnc_id": 28862,
"hgvs_c": "c.1808delA",
"hgvs_p": "p.Lys603fs",
"transcript": "NM_133433.4",
"protein_id": "NP_597677.2",
"transcript_support_level": null,
"aa_start": 603,
"aa_end": null,
"aa_length": 2804,
"cds_start": 1808,
"cds_end": null,
"cds_length": 8415,
"cdna_start": 2297,
"cdna_end": null,
"cdna_length": 10425,
"mane_select": "ENST00000282516.13",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 47,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NIPBL",
"gene_hgnc_id": 28862,
"hgvs_c": "c.1808delA",
"hgvs_p": "p.Lys603fs",
"transcript": "ENST00000282516.13",
"protein_id": "ENSP00000282516.8",
"transcript_support_level": 1,
"aa_start": 603,
"aa_end": null,
"aa_length": 2804,
"cds_start": 1808,
"cds_end": null,
"cds_length": 8415,
"cdna_start": 2297,
"cdna_end": null,
"cdna_length": 10425,
"mane_select": "NM_133433.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 46,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NIPBL",
"gene_hgnc_id": 28862,
"hgvs_c": "c.1808delA",
"hgvs_p": "p.Lys603fs",
"transcript": "ENST00000448238.2",
"protein_id": "ENSP00000406266.2",
"transcript_support_level": 1,
"aa_start": 603,
"aa_end": null,
"aa_length": 2697,
"cds_start": 1808,
"cds_end": null,
"cds_length": 8094,
"cdna_start": 2276,
"cdna_end": null,
"cdna_length": 8729,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 47,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NIPBL",
"gene_hgnc_id": 28862,
"hgvs_c": "c.1808delA",
"hgvs_p": "p.Lys603fs",
"transcript": "NM_001438586.1",
"protein_id": "NP_001425515.1",
"transcript_support_level": null,
"aa_start": 603,
"aa_end": null,
"aa_length": 2698,
"cds_start": 1808,
"cds_end": null,
"cds_length": 8097,
"cdna_start": 2297,
"cdna_end": null,
"cdna_length": 10466,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 46,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NIPBL",
"gene_hgnc_id": 28862,
"hgvs_c": "c.1808delA",
"hgvs_p": "p.Lys603fs",
"transcript": "NM_015384.5",
"protein_id": "NP_056199.2",
"transcript_support_level": null,
"aa_start": 603,
"aa_end": null,
"aa_length": 2697,
"cds_start": 1808,
"cds_end": null,
"cds_length": 8094,
"cdna_start": 2297,
"cdna_end": null,
"cdna_length": 10379,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 46,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NIPBL",
"gene_hgnc_id": 28862,
"hgvs_c": "c.1808delA",
"hgvs_p": "p.Lys603fs",
"transcript": "ENST00000652901.1",
"protein_id": "ENSP00000499536.1",
"transcript_support_level": null,
"aa_start": 603,
"aa_end": null,
"aa_length": 2649,
"cds_start": 1808,
"cds_end": null,
"cds_length": 7950,
"cdna_start": 2225,
"cdna_end": null,
"cdna_length": 9228,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 46,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NIPBL",
"gene_hgnc_id": 28862,
"hgvs_c": "c.1808delA",
"hgvs_p": "p.Lys603fs",
"transcript": "XM_006714467.3",
"protein_id": "XP_006714530.1",
"transcript_support_level": null,
"aa_start": 603,
"aa_end": null,
"aa_length": 2755,
"cds_start": 1808,
"cds_end": null,
"cds_length": 8268,
"cdna_start": 2297,
"cdna_end": null,
"cdna_length": 10278,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 46,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NIPBL",
"gene_hgnc_id": 28862,
"hgvs_c": "c.1808delA",
"hgvs_p": "p.Lys603fs",
"transcript": "XM_006714468.3",
"protein_id": "XP_006714531.1",
"transcript_support_level": null,
"aa_start": 603,
"aa_end": null,
"aa_length": 2738,
"cds_start": 1808,
"cds_end": null,
"cds_length": 8217,
"cdna_start": 2297,
"cdna_end": null,
"cdna_length": 10227,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 46,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NIPBL",
"gene_hgnc_id": 28862,
"hgvs_c": "c.1808delA",
"hgvs_p": "p.Lys603fs",
"transcript": "XM_017009329.2",
"protein_id": "XP_016864818.1",
"transcript_support_level": null,
"aa_start": 603,
"aa_end": null,
"aa_length": 2649,
"cds_start": 1808,
"cds_end": null,
"cds_length": 7950,
"cdna_start": 2297,
"cdna_end": null,
"cdna_length": 10319,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 41,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NIPBL",
"gene_hgnc_id": 28862,
"hgvs_c": "c.1148delA",
"hgvs_p": "p.Lys383fs",
"transcript": "XM_005248282.6",
"protein_id": "XP_005248339.3",
"transcript_support_level": null,
"aa_start": 383,
"aa_end": null,
"aa_length": 2584,
"cds_start": 1148,
"cds_end": null,
"cds_length": 7755,
"cdna_start": 1852,
"cdna_end": null,
"cdna_length": 9980,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 43,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NIPBL",
"gene_hgnc_id": 28862,
"hgvs_c": "c.1808delA",
"hgvs_p": "p.Lys603fs",
"transcript": "XM_011514015.2",
"protein_id": "XP_011512317.1",
"transcript_support_level": null,
"aa_start": 603,
"aa_end": null,
"aa_length": 2421,
"cds_start": 1808,
"cds_end": null,
"cds_length": 7266,
"cdna_start": 2297,
"cdna_end": null,
"cdna_length": 7895,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"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": "NIPBL",
"gene_hgnc_id": 28862,
"hgvs_c": "n.1428delA",
"hgvs_p": null,
"transcript": "ENST00000504430.5",
"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": 3455,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "NIPBL",
"gene_hgnc_id": 28862,
"dbsnp": "rs727503767",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": 0,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 0,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"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": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 6.801,
"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": 18,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 18,
"benign_score": 0,
"pathogenic_score": 18,
"criteria": [
"PVS1",
"PM2",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000282516.13",
"gene_symbol": "NIPBL",
"hgnc_id": 28862,
"effects": [
"frameshift_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.1808delA",
"hgvs_p": "p.Lys603fs"
}
],
"clinvar_disease": "Cornelia de Lange syndrome 1,not provided",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:1 LP:1",
"phenotype_combined": "Cornelia de Lange syndrome 1|not provided",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}