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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: 1-248917034-T-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=248917034&ref=T&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 248917034,
"ref": "T",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_170725.3",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGBD2",
"gene_hgnc_id": 19399,
"hgvs_c": "c.450T>A",
"hgvs_p": "p.Asp150Glu",
"transcript": "NM_170725.3",
"protein_id": "NP_733843.1",
"transcript_support_level": null,
"aa_start": 150,
"aa_end": null,
"aa_length": 592,
"cds_start": 450,
"cds_end": null,
"cds_length": 1779,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000329291.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_170725.3"
},
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGBD2",
"gene_hgnc_id": 19399,
"hgvs_c": "c.450T>A",
"hgvs_p": "p.Asp150Glu",
"transcript": "ENST00000329291.6",
"protein_id": "ENSP00000331643.5",
"transcript_support_level": 1,
"aa_start": 150,
"aa_end": null,
"aa_length": 592,
"cds_start": 450,
"cds_end": null,
"cds_length": 1779,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_170725.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000329291.6"
},
{
"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": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PGBD2",
"gene_hgnc_id": 19399,
"hgvs_c": "c.-59-245T>A",
"hgvs_p": null,
"transcript": "ENST00000355360.8",
"protein_id": "ENSP00000355424.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 341,
"cds_start": null,
"cds_end": null,
"cds_length": 1026,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000355360.8"
},
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGBD2",
"gene_hgnc_id": 19399,
"hgvs_c": "c.450T>A",
"hgvs_p": "p.Asp150Glu",
"transcript": "ENST00000935434.1",
"protein_id": "ENSP00000605493.1",
"transcript_support_level": null,
"aa_start": 150,
"aa_end": null,
"aa_length": 592,
"cds_start": 450,
"cds_end": null,
"cds_length": 1779,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000935434.1"
},
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGBD2",
"gene_hgnc_id": 19399,
"hgvs_c": "c.450T>A",
"hgvs_p": "p.Asp150Glu",
"transcript": "XM_011544159.3",
"protein_id": "XP_011542461.1",
"transcript_support_level": null,
"aa_start": 150,
"aa_end": null,
"aa_length": 592,
"cds_start": 450,
"cds_end": null,
"cds_length": 1779,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011544159.3"
},
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGBD2",
"gene_hgnc_id": 19399,
"hgvs_c": "c.450T>A",
"hgvs_p": "p.Asp150Glu",
"transcript": "XM_011544161.4",
"protein_id": "XP_011542463.1",
"transcript_support_level": null,
"aa_start": 150,
"aa_end": null,
"aa_length": 592,
"cds_start": 450,
"cds_end": null,
"cds_length": 1779,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011544161.4"
},
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGBD2",
"gene_hgnc_id": 19399,
"hgvs_c": "c.441T>A",
"hgvs_p": "p.Asp147Glu",
"transcript": "XM_047417842.1",
"protein_id": "XP_047273798.1",
"transcript_support_level": null,
"aa_start": 147,
"aa_end": null,
"aa_length": 589,
"cds_start": 441,
"cds_end": null,
"cds_length": 1770,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047417842.1"
},
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGBD2",
"gene_hgnc_id": 19399,
"hgvs_c": "c.450T>A",
"hgvs_p": "p.Asp150Glu",
"transcript": "XM_047417845.1",
"protein_id": "XP_047273801.1",
"transcript_support_level": null,
"aa_start": 150,
"aa_end": null,
"aa_length": 276,
"cds_start": 450,
"cds_end": null,
"cds_length": 831,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047417845.1"
},
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGBD2",
"gene_hgnc_id": 19399,
"hgvs_c": "c.450T>A",
"hgvs_p": "p.Asp150Glu",
"transcript": "XM_047417849.1",
"protein_id": "XP_047273805.1",
"transcript_support_level": null,
"aa_start": 150,
"aa_end": null,
"aa_length": 272,
"cds_start": 450,
"cds_end": null,
"cds_length": 819,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047417849.1"
},
{
"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": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PGBD2",
"gene_hgnc_id": 19399,
"hgvs_c": "c.-59-245T>A",
"hgvs_p": null,
"transcript": "NM_001017434.2",
"protein_id": "NP_001017434.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 341,
"cds_start": null,
"cds_end": null,
"cds_length": 1026,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001017434.2"
},
{
"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": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PGBD2",
"gene_hgnc_id": 19399,
"hgvs_c": "c.-59-245T>A",
"hgvs_p": null,
"transcript": "XM_047417844.1",
"protein_id": "XP_047273800.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 341,
"cds_start": null,
"cds_end": null,
"cds_length": 1026,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047417844.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PGBD2",
"gene_hgnc_id": 19399,
"hgvs_c": "n.160-245T>A",
"hgvs_p": null,
"transcript": "ENST00000462488.1",
"protein_id": null,
"transcript_support_level": 5,
"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": "ENST00000462488.1"
}
],
"gene_symbol": "PGBD2",
"gene_hgnc_id": 19399,
"dbsnp": "rs748260058",
"frequency_reference_population": 0.0000037181126,
"hom_count_reference_population": 0,
"allele_count_reference_population": 6,
"gnomad_exomes_af": 0.00000205256,
"gnomad_genomes_af": 0.0000197197,
"gnomad_exomes_ac": 3,
"gnomad_genomes_ac": 3,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.44587504863739014,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.289,
"revel_prediction": "Benign",
"alphamissense_score": 0.5273,
"alphamissense_prediction": "Uncertain_significance",
"bayesdelnoaf_score": -0.36,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.04,
"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": 2,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "NM_170725.3",
"gene_symbol": "PGBD2",
"hgnc_id": 19399,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.450T>A",
"hgvs_p": "p.Asp150Glu"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}