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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: 20-3889134-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=20&pos=3889134&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "20",
"pos": 3889134,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_153638.4",
"consequences": [
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PANK2",
"gene_hgnc_id": 15894,
"hgvs_c": "c.34C>T",
"hgvs_p": "p.His12Tyr",
"transcript": "ENST00000316562.9",
"protein_id": "ENSP00000313377.4",
"transcript_support_level": 1,
"aa_start": 12,
"aa_end": null,
"aa_length": 570,
"cds_start": 34,
"cds_end": null,
"cds_length": 1713,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000316562.9"
},
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PANK2",
"gene_hgnc_id": 15894,
"hgvs_c": "c.34C>T",
"hgvs_p": "p.His12Tyr",
"transcript": "NM_153638.4",
"protein_id": "NP_705902.2",
"transcript_support_level": null,
"aa_start": 12,
"aa_end": null,
"aa_length": 570,
"cds_start": 34,
"cds_end": null,
"cds_length": 1713,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_153638.4"
},
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PANK2",
"gene_hgnc_id": 15894,
"hgvs_c": "c.34C>T",
"hgvs_p": "p.His12Tyr",
"transcript": "NM_001324192.1",
"protein_id": "NP_001311121.1",
"transcript_support_level": null,
"aa_start": 12,
"aa_end": null,
"aa_length": 331,
"cds_start": 34,
"cds_end": null,
"cds_length": 996,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001324192.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PANK2",
"gene_hgnc_id": 15894,
"hgvs_c": "c.-246+230C>T",
"hgvs_p": null,
"transcript": "NM_024960.6",
"protein_id": "NP_079236.3",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 279,
"cds_start": null,
"cds_end": null,
"cds_length": 840,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_024960.6"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PANK2",
"gene_hgnc_id": 15894,
"hgvs_c": "c.-246+230C>T",
"hgvs_p": null,
"transcript": "ENST00000497424.5",
"protein_id": "ENSP00000417609.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 279,
"cds_start": null,
"cds_end": null,
"cds_length": 840,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000497424.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PANK2",
"gene_hgnc_id": 15894,
"hgvs_c": "c.-538+118C>T",
"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": null,
"cds_end": null,
"cds_length": 347,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000495692.5"
},
{
"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": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PANK2-AS1",
"gene_hgnc_id": 40732,
"hgvs_c": "n.69G>A",
"hgvs_p": null,
"transcript": "ENST00000451507.2",
"protein_id": null,
"transcript_support_level": 2,
"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": "pseudogene",
"feature": "ENST00000451507.2"
},
{
"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": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PANK2-AS1",
"gene_hgnc_id": 40732,
"hgvs_c": "n.40G>A",
"hgvs_p": null,
"transcript": "ENST00000702266.2",
"protein_id": null,
"transcript_support_level": null,
"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": "pseudogene",
"feature": "ENST00000702266.2"
},
{
"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": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PANK2-AS1",
"gene_hgnc_id": 40732,
"hgvs_c": "n.30G>A",
"hgvs_p": null,
"transcript": "ENST00000725518.1",
"protein_id": null,
"transcript_support_level": null,
"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": "pseudogene",
"feature": "ENST00000725518.1"
},
{
"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": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PANK2-AS1",
"gene_hgnc_id": 40732,
"hgvs_c": "n.64G>A",
"hgvs_p": null,
"transcript": "ENST00000725519.1",
"protein_id": null,
"transcript_support_level": null,
"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": "pseudogene",
"feature": "ENST00000725519.1"
},
{
"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": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PANK2-AS1",
"gene_hgnc_id": 40732,
"hgvs_c": "n.40G>A",
"hgvs_p": null,
"transcript": "XR_001754478.3",
"protein_id": null,
"transcript_support_level": null,
"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": "pseudogene",
"feature": "XR_001754478.3"
}
],
"gene_symbol": "PANK2",
"gene_hgnc_id": 15894,
"dbsnp": "rs374286033",
"frequency_reference_population": 0.00007233704,
"hom_count_reference_population": 1,
"allele_count_reference_population": 113,
"gnomad_exomes_af": 0.0000404313,
"gnomad_genomes_af": 0.000367618,
"gnomad_exomes_ac": 57,
"gnomad_genomes_ac": 56,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.03422313928604126,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.317,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.095,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.11,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.301,
"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": -8,
"acmg_classification": "Benign",
"acmg_criteria": "PP2,BP4_Strong,BP6,BS1",
"acmg_by_gene": [
{
"score": -8,
"benign_score": 9,
"pathogenic_score": 1,
"criteria": [
"PP2",
"BP4_Strong",
"BP6",
"BS1"
],
"verdict": "Benign",
"transcript": "NM_153638.4",
"gene_symbol": "PANK2",
"hgnc_id": 15894,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.34C>T",
"hgvs_p": "p.His12Tyr"
},
{
"score": -5,
"benign_score": 5,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6"
],
"verdict": "Likely_benign",
"transcript": "ENST00000451507.2",
"gene_symbol": "PANK2-AS1",
"hgnc_id": 40732,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.69G>A",
"hgvs_p": null
}
],
"clinvar_disease": "Inborn genetic diseases,Pigmentary pallidal degeneration,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:2 LB:1",
"phenotype_combined": "Pigmentary pallidal degeneration|Inborn genetic diseases|not specified",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}