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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: 20-3910728-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=20&pos=3910728&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "20",
"pos": 3910728,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000610179.7",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PANK2",
"gene_hgnc_id": 15894,
"hgvs_c": "c.803A>G",
"hgvs_p": "p.Asp268Gly",
"transcript": "NM_001386393.1",
"protein_id": "NP_001373322.1",
"transcript_support_level": null,
"aa_start": 268,
"aa_end": null,
"aa_length": 460,
"cds_start": 803,
"cds_end": null,
"cds_length": 1383,
"cdna_start": 847,
"cdna_end": null,
"cdna_length": 8020,
"mane_select": "ENST00000610179.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PANK2",
"gene_hgnc_id": 15894,
"hgvs_c": "c.803A>G",
"hgvs_p": "p.Asp268Gly",
"transcript": "ENST00000610179.7",
"protein_id": "ENSP00000477429.2",
"transcript_support_level": 1,
"aa_start": 268,
"aa_end": null,
"aa_length": 460,
"cds_start": 803,
"cds_end": null,
"cds_length": 1383,
"cdna_start": 847,
"cdna_end": null,
"cdna_length": 8020,
"mane_select": "NM_001386393.1",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PANK2",
"gene_hgnc_id": 15894,
"hgvs_c": "c.1133A>G",
"hgvs_p": "p.Asp378Gly",
"transcript": "ENST00000316562.9",
"protein_id": "ENSP00000313377.4",
"transcript_support_level": 1,
"aa_start": 378,
"aa_end": null,
"aa_length": 570,
"cds_start": 1133,
"cds_end": null,
"cds_length": 1713,
"cdna_start": 1311,
"cdna_end": null,
"cdna_length": 8484,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PANK2",
"gene_hgnc_id": 15894,
"hgvs_c": "c.260A>G",
"hgvs_p": "p.Asp87Gly",
"transcript": "ENST00000621507.1",
"protein_id": "ENSP00000481523.1",
"transcript_support_level": 1,
"aa_start": 87,
"aa_end": null,
"aa_length": 279,
"cds_start": 260,
"cds_end": null,
"cds_length": 840,
"cdna_start": 622,
"cdna_end": null,
"cdna_length": 1763,
"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": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PANK2",
"gene_hgnc_id": 15894,
"hgvs_c": "n.*144A>G",
"hgvs_p": null,
"transcript": "ENST00000336066.8",
"protein_id": "ENSP00000477229.2",
"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": 1843,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PANK2",
"gene_hgnc_id": 15894,
"hgvs_c": "n.*144A>G",
"hgvs_p": null,
"transcript": "ENST00000336066.8",
"protein_id": "ENSP00000477229.2",
"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": 1843,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PANK2",
"gene_hgnc_id": 15894,
"hgvs_c": "c.1133A>G",
"hgvs_p": "p.Asp378Gly",
"transcript": "NM_153638.4",
"protein_id": "NP_705902.2",
"transcript_support_level": null,
"aa_start": 378,
"aa_end": null,
"aa_length": 570,
"cds_start": 1133,
"cds_end": null,
"cds_length": 1713,
"cdna_start": 1311,
"cdna_end": null,
"cdna_length": 8484,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PANK2",
"gene_hgnc_id": 15894,
"hgvs_c": "c.629A>G",
"hgvs_p": "p.Asp210Gly",
"transcript": "ENST00000646394.1",
"protein_id": "ENSP00000496112.1",
"transcript_support_level": null,
"aa_start": 210,
"aa_end": null,
"aa_length": 402,
"cds_start": 629,
"cds_end": null,
"cds_length": 1209,
"cdna_start": 630,
"cdna_end": null,
"cdna_length": 1547,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PANK2",
"gene_hgnc_id": 15894,
"hgvs_c": "c.260A>G",
"hgvs_p": "p.Asp87Gly",
"transcript": "NM_001324191.2",
"protein_id": "NP_001311120.1",
"transcript_support_level": null,
"aa_start": 87,
"aa_end": null,
"aa_length": 279,
"cds_start": 260,
"cds_end": null,
"cds_length": 840,
"cdna_start": 1015,
"cdna_end": null,
"cdna_length": 8188,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PANK2",
"gene_hgnc_id": 15894,
"hgvs_c": "c.260A>G",
"hgvs_p": "p.Asp87Gly",
"transcript": "NM_024960.6",
"protein_id": "NP_079236.3",
"transcript_support_level": null,
"aa_start": 87,
"aa_end": null,
"aa_length": 279,
"cds_start": 260,
"cds_end": null,
"cds_length": 840,
"cdna_start": 629,
"cdna_end": null,
"cdna_length": 7802,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PANK2",
"gene_hgnc_id": 15894,
"hgvs_c": "c.260A>G",
"hgvs_p": "p.Asp87Gly",
"transcript": "NM_153640.4",
"protein_id": "NP_705904.1",
"transcript_support_level": null,
"aa_start": 87,
"aa_end": null,
"aa_length": 279,
"cds_start": 260,
"cds_end": null,
"cds_length": 840,
"cdna_start": 622,
"cdna_end": null,
"cdna_length": 7795,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PANK2",
"gene_hgnc_id": 15894,
"hgvs_c": "c.260A>G",
"hgvs_p": "p.Asp87Gly",
"transcript": "ENST00000497424.5",
"protein_id": "ENSP00000417609.1",
"transcript_support_level": 2,
"aa_start": 87,
"aa_end": null,
"aa_length": 279,
"cds_start": 260,
"cds_end": null,
"cds_length": 840,
"cdna_start": 571,
"cdna_end": null,
"cdna_length": 4815,
"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": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PANK2",
"gene_hgnc_id": 15894,
"hgvs_c": "n.368A>G",
"hgvs_p": null,
"transcript": "ENST00000464452.1",
"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": 771,
"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": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PANK2",
"gene_hgnc_id": 15894,
"hgvs_c": "n.534A>G",
"hgvs_p": null,
"transcript": "ENST00000471830.1",
"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": 622,
"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": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PANK2",
"gene_hgnc_id": 15894,
"hgvs_c": "n.*433A>G",
"hgvs_p": null,
"transcript": "ENST00000643504.2",
"protein_id": "ENSP00000495157.2",
"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": 5127,
"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": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PANK2",
"gene_hgnc_id": 15894,
"hgvs_c": "n.704A>G",
"hgvs_p": null,
"transcript": "NR_136715.2",
"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": 7877,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PANK2",
"gene_hgnc_id": 15894,
"hgvs_c": "c.-176A>G",
"hgvs_p": null,
"transcript": "NM_001324193.2",
"protein_id": "NP_001311122.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 134,
"cds_start": -4,
"cds_end": null,
"cds_length": 405,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 7652,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PANK2",
"gene_hgnc_id": 15894,
"hgvs_c": "c.-176A>G",
"hgvs_p": null,
"transcript": "ENST00000495692.5",
"protein_id": "ENSP00000476745.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 114,
"cds_start": -4,
"cds_end": null,
"cds_length": 347,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 967,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PANK2",
"gene_hgnc_id": 15894,
"hgvs_c": "n.*433A>G",
"hgvs_p": null,
"transcript": "ENST00000643504.2",
"protein_id": "ENSP00000495157.2",
"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": 5127,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PANK2",
"gene_hgnc_id": 15894,
"dbsnp": "rs562740927",
"frequency_reference_population": 0.000046463854,
"hom_count_reference_population": 0,
"allele_count_reference_population": 75,
"gnomad_exomes_af": 0.0000430957,
"gnomad_genomes_af": 0.0000787939,
"gnomad_exomes_ac": 63,
"gnomad_genomes_ac": 12,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.08382576704025269,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.69,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.3525,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.16,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 2.091,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.01,
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PP2,PP5,BP4,BS1_Supporting",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PP2",
"PP5",
"BP4",
"BS1_Supporting"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000610179.7",
"gene_symbol": "PANK2",
"hgnc_id": 15894,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.803A>G",
"hgvs_p": "p.Asp268Gly"
}
],
"clinvar_disease": "Pigmentary pallidal degeneration,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "P:2 LP:2 US:2",
"phenotype_combined": "Pigmentary pallidal degeneration|not provided",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}