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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: 1-2406561-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=2406561&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 2406561,
"ref": "C",
"alt": "A",
"effect": "stop_gained",
"transcript": "ENST00000447513.7",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"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.835G>T",
"hgvs_p": "p.Glu279*",
"transcript": "NM_002617.4",
"protein_id": "NP_002608.1",
"transcript_support_level": null,
"aa_start": 279,
"aa_end": null,
"aa_length": 326,
"cds_start": 835,
"cds_end": null,
"cds_length": 981,
"cdna_start": 897,
"cdna_end": null,
"cdna_length": 2835,
"mane_select": "ENST00000447513.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"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.835G>T",
"hgvs_p": "p.Glu279*",
"transcript": "ENST00000447513.7",
"protein_id": "ENSP00000407922.2",
"transcript_support_level": 1,
"aa_start": 279,
"aa_end": null,
"aa_length": 326,
"cds_start": 835,
"cds_end": null,
"cds_length": 981,
"cdna_start": 897,
"cdna_end": null,
"cdna_length": 2835,
"mane_select": "NM_002617.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"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.895G>T",
"hgvs_p": "p.Glu299*",
"transcript": "ENST00000288774.8",
"protein_id": "ENSP00000288774.3",
"transcript_support_level": 1,
"aa_start": 299,
"aa_end": null,
"aa_length": 346,
"cds_start": 895,
"cds_end": null,
"cds_length": 1041,
"cdna_start": 957,
"cdna_end": null,
"cdna_length": 2905,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"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.895G>T",
"hgvs_p": "p.Glu299*",
"transcript": "NM_153818.2",
"protein_id": "NP_722540.1",
"transcript_support_level": null,
"aa_start": 299,
"aa_end": null,
"aa_length": 346,
"cds_start": 895,
"cds_end": null,
"cds_length": 1041,
"cdna_start": 957,
"cdna_end": null,
"cdna_length": 2895,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"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.892G>T",
"hgvs_p": "p.Glu298*",
"transcript": "NM_001374425.1",
"protein_id": "NP_001361354.1",
"transcript_support_level": null,
"aa_start": 298,
"aa_end": null,
"aa_length": 345,
"cds_start": 892,
"cds_end": null,
"cds_length": 1038,
"cdna_start": 954,
"cdna_end": null,
"cdna_length": 2892,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"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.835G>T",
"hgvs_p": "p.Glu279*",
"transcript": "ENST00000507596.5",
"protein_id": "ENSP00000424291.1",
"transcript_support_level": 5,
"aa_start": 279,
"aa_end": null,
"aa_length": 324,
"cds_start": 835,
"cds_end": null,
"cds_length": 975,
"cdna_start": 873,
"cdna_end": null,
"cdna_length": 1941,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"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.460G>T",
"hgvs_p": "p.Glu154*",
"transcript": "NM_001374426.1",
"protein_id": "NP_001361355.1",
"transcript_support_level": null,
"aa_start": 154,
"aa_end": null,
"aa_length": 201,
"cds_start": 460,
"cds_end": null,
"cds_length": 606,
"cdna_start": 1011,
"cdna_end": null,
"cdna_length": 2949,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"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.403G>T",
"hgvs_p": "p.Glu135*",
"transcript": "NM_001374427.1",
"protein_id": "NP_001361356.1",
"transcript_support_level": null,
"aa_start": 135,
"aa_end": null,
"aa_length": 182,
"cds_start": 403,
"cds_end": null,
"cds_length": 549,
"cdna_start": 954,
"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.*201G>T",
"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.787G>T",
"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.950G>T",
"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.*201G>T",
"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.*301G>T",
"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": "rs62641225",
"frequency_reference_population": 0.0000020533712,
"hom_count_reference_population": 0,
"allele_count_reference_population": 3,
"gnomad_exomes_af": 0.00000205337,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 3,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.5099999904632568,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"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": 0.51,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 3.614,
"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": 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": "ENST00000447513.7",
"gene_symbol": "PEX10",
"hgnc_id": 8851,
"effects": [
"stop_gained"
],
"inheritance_mode": "AR",
"hgvs_c": "c.835G>T",
"hgvs_p": "p.Glu279*"
}
],
"clinvar_disease": " complementation group 7,Peroxisome biogenesis disorder,Peroxisome biogenesis disorder 6A (Zellweger),Zellweger spectrum disorders,not provided",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:3 LP:1",
"phenotype_combined": "not provided|Peroxisome biogenesis disorder, complementation group 7|Zellweger spectrum disorders|Peroxisome biogenesis disorder 6A (Zellweger)|Peroxisome biogenesis disorder",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}