← Back to variant description
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: 1-2406528-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=2406528&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 2406528,
"ref": "G",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000447513.7",
"consequences": [
{
"aa_ref": "H",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX10",
"gene_hgnc_id": 8851,
"hgvs_c": "c.868C>G",
"hgvs_p": "p.His290Asp",
"transcript": "NM_002617.4",
"protein_id": "NP_002608.1",
"transcript_support_level": null,
"aa_start": 290,
"aa_end": null,
"aa_length": 326,
"cds_start": 868,
"cds_end": null,
"cds_length": 981,
"cdna_start": 930,
"cdna_end": null,
"cdna_length": 2835,
"mane_select": "ENST00000447513.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "D",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX10",
"gene_hgnc_id": 8851,
"hgvs_c": "c.868C>G",
"hgvs_p": "p.His290Asp",
"transcript": "ENST00000447513.7",
"protein_id": "ENSP00000407922.2",
"transcript_support_level": 1,
"aa_start": 290,
"aa_end": null,
"aa_length": 326,
"cds_start": 868,
"cds_end": null,
"cds_length": 981,
"cdna_start": 930,
"cdna_end": null,
"cdna_length": 2835,
"mane_select": "NM_002617.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX10",
"gene_hgnc_id": 8851,
"hgvs_c": "c.928C>G",
"hgvs_p": "p.His310Asp",
"transcript": "ENST00000288774.8",
"protein_id": "ENSP00000288774.3",
"transcript_support_level": 1,
"aa_start": 310,
"aa_end": null,
"aa_length": 346,
"cds_start": 928,
"cds_end": null,
"cds_length": 1041,
"cdna_start": 990,
"cdna_end": null,
"cdna_length": 2905,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX10",
"gene_hgnc_id": 8851,
"hgvs_c": "c.928C>G",
"hgvs_p": "p.His310Asp",
"transcript": "NM_153818.2",
"protein_id": "NP_722540.1",
"transcript_support_level": null,
"aa_start": 310,
"aa_end": null,
"aa_length": 346,
"cds_start": 928,
"cds_end": null,
"cds_length": 1041,
"cdna_start": 990,
"cdna_end": null,
"cdna_length": 2895,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX10",
"gene_hgnc_id": 8851,
"hgvs_c": "c.925C>G",
"hgvs_p": "p.His309Asp",
"transcript": "NM_001374425.1",
"protein_id": "NP_001361354.1",
"transcript_support_level": null,
"aa_start": 309,
"aa_end": null,
"aa_length": 345,
"cds_start": 925,
"cds_end": null,
"cds_length": 1038,
"cdna_start": 987,
"cdna_end": null,
"cdna_length": 2892,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX10",
"gene_hgnc_id": 8851,
"hgvs_c": "c.868C>G",
"hgvs_p": "p.His290Asp",
"transcript": "ENST00000507596.5",
"protein_id": "ENSP00000424291.1",
"transcript_support_level": 5,
"aa_start": 290,
"aa_end": null,
"aa_length": 324,
"cds_start": 868,
"cds_end": null,
"cds_length": 975,
"cdna_start": 906,
"cdna_end": null,
"cdna_length": 1941,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX10",
"gene_hgnc_id": 8851,
"hgvs_c": "c.493C>G",
"hgvs_p": "p.His165Asp",
"transcript": "NM_001374426.1",
"protein_id": "NP_001361355.1",
"transcript_support_level": null,
"aa_start": 165,
"aa_end": null,
"aa_length": 201,
"cds_start": 493,
"cds_end": null,
"cds_length": 606,
"cdna_start": 1044,
"cdna_end": null,
"cdna_length": 2949,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX10",
"gene_hgnc_id": 8851,
"hgvs_c": "c.436C>G",
"hgvs_p": "p.His146Asp",
"transcript": "NM_001374427.1",
"protein_id": "NP_001361356.1",
"transcript_support_level": null,
"aa_start": 146,
"aa_end": null,
"aa_length": 182,
"cds_start": 436,
"cds_end": null,
"cds_length": 549,
"cdna_start": 987,
"cdna_end": null,
"cdna_length": 2892,
"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": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX10",
"gene_hgnc_id": 8851,
"hgvs_c": "n.*234C>G",
"hgvs_p": null,
"transcript": "ENST00000510434.1",
"protein_id": "ENSP00000423051.1",
"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": 907,
"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": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX10",
"gene_hgnc_id": 8851,
"hgvs_c": "n.820C>G",
"hgvs_p": null,
"transcript": "ENST00000650293.1",
"protein_id": "ENSP00000497980.1",
"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": 2260,
"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": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX10",
"gene_hgnc_id": 8851,
"hgvs_c": "n.983C>G",
"hgvs_p": null,
"transcript": "NR_164636.1",
"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": 2888,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX10",
"gene_hgnc_id": 8851,
"hgvs_c": "n.*234C>G",
"hgvs_p": null,
"transcript": "ENST00000510434.1",
"protein_id": "ENSP00000423051.1",
"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": 907,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX10",
"gene_hgnc_id": 8851,
"hgvs_c": "c.*334C>G",
"hgvs_p": null,
"transcript": "XM_047422539.1",
"protein_id": "XP_047278495.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 209,
"cds_start": -4,
"cds_end": null,
"cds_length": 630,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 831,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PEX10",
"gene_hgnc_id": 8851,
"dbsnp": "rs61752094",
"frequency_reference_population": 0.0000024797098,
"hom_count_reference_population": 0,
"allele_count_reference_population": 4,
"gnomad_exomes_af": 6.8452e-7,
"gnomad_genomes_af": 0.0000197091,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": 3,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9903566837310791,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.988,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9841,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.55,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 9.33,
"phylop100way_prediction": "Pathogenic",
"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": 9,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PM5,PP3_Strong,PP5",
"acmg_by_gene": [
{
"score": 9,
"benign_score": 0,
"pathogenic_score": 9,
"criteria": [
"PM2",
"PM5",
"PP3_Strong",
"PP5"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000447513.7",
"gene_symbol": "PEX10",
"hgnc_id": 8851,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.868C>G",
"hgvs_p": "p.His290Asp"
}
],
"clinvar_disease": " complementation group 7,Peroxisome biogenesis disorder,Peroxisome biogenesis disorder 6A (Zellweger),Peroxisome biogenesis disorder 6B",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "LP:1 US:1",
"phenotype_combined": "Peroxisome biogenesis disorder 6A (Zellweger);Peroxisome biogenesis disorder 6B|Peroxisome biogenesis disorder, complementation group 7|Peroxisome biogenesis disorder 6A (Zellweger)",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}