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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: 6-42965726-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=42965726&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "6",
"pos": 42965726,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_000287.4",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX6",
"gene_hgnc_id": 8859,
"hgvs_c": "c.2426C>T",
"hgvs_p": "p.Ala809Val",
"transcript": "NM_000287.4",
"protein_id": "NP_000278.3",
"transcript_support_level": null,
"aa_start": 809,
"aa_end": null,
"aa_length": 980,
"cds_start": 2426,
"cds_end": null,
"cds_length": 2943,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000304611.13",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_000287.4"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX6",
"gene_hgnc_id": 8859,
"hgvs_c": "c.2426C>T",
"hgvs_p": "p.Ala809Val",
"transcript": "ENST00000304611.13",
"protein_id": "ENSP00000303511.8",
"transcript_support_level": 1,
"aa_start": 809,
"aa_end": null,
"aa_length": 980,
"cds_start": 2426,
"cds_end": null,
"cds_length": 2943,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_000287.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000304611.13"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX6",
"gene_hgnc_id": 8859,
"hgvs_c": "c.2179C>T",
"hgvs_p": "p.Pro727Ser",
"transcript": "ENST00000244546.4",
"protein_id": "ENSP00000244546.4",
"transcript_support_level": 1,
"aa_start": 727,
"aa_end": null,
"aa_length": 738,
"cds_start": 2179,
"cds_end": null,
"cds_length": 2217,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000244546.4"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX6",
"gene_hgnc_id": 8859,
"hgvs_c": "c.2465C>T",
"hgvs_p": "p.Ala822Val",
"transcript": "ENST00000858656.1",
"protein_id": "ENSP00000528715.1",
"transcript_support_level": null,
"aa_start": 822,
"aa_end": null,
"aa_length": 993,
"cds_start": 2465,
"cds_end": null,
"cds_length": 2982,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000858656.1"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX6",
"gene_hgnc_id": 8859,
"hgvs_c": "c.2447C>T",
"hgvs_p": "p.Ala816Val",
"transcript": "ENST00000858658.1",
"protein_id": "ENSP00000528717.1",
"transcript_support_level": null,
"aa_start": 816,
"aa_end": null,
"aa_length": 987,
"cds_start": 2447,
"cds_end": null,
"cds_length": 2964,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000858658.1"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX6",
"gene_hgnc_id": 8859,
"hgvs_c": "c.2426C>T",
"hgvs_p": "p.Ala809Val",
"transcript": "ENST00000970120.1",
"protein_id": "ENSP00000640179.1",
"transcript_support_level": null,
"aa_start": 809,
"aa_end": null,
"aa_length": 980,
"cds_start": 2426,
"cds_end": null,
"cds_length": 2943,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000970120.1"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX6",
"gene_hgnc_id": 8859,
"hgvs_c": "c.2426C>T",
"hgvs_p": "p.Ala809Val",
"transcript": "ENST00000858654.1",
"protein_id": "ENSP00000528713.1",
"transcript_support_level": null,
"aa_start": 809,
"aa_end": null,
"aa_length": 954,
"cds_start": 2426,
"cds_end": null,
"cds_length": 2865,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000858654.1"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX6",
"gene_hgnc_id": 8859,
"hgvs_c": "c.2342C>T",
"hgvs_p": "p.Ala781Val",
"transcript": "ENST00000858653.1",
"protein_id": "ENSP00000528712.1",
"transcript_support_level": null,
"aa_start": 781,
"aa_end": null,
"aa_length": 952,
"cds_start": 2342,
"cds_end": null,
"cds_length": 2859,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000858653.1"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX6",
"gene_hgnc_id": 8859,
"hgvs_c": "c.2162C>T",
"hgvs_p": "p.Ala721Val",
"transcript": "NM_001316313.2",
"protein_id": "NP_001303242.1",
"transcript_support_level": null,
"aa_start": 721,
"aa_end": null,
"aa_length": 892,
"cds_start": 2162,
"cds_end": null,
"cds_length": 2679,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001316313.2"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX6",
"gene_hgnc_id": 8859,
"hgvs_c": "c.2162C>T",
"hgvs_p": "p.Ala721Val",
"transcript": "ENST00000858651.1",
"protein_id": "ENSP00000528710.1",
"transcript_support_level": null,
"aa_start": 721,
"aa_end": null,
"aa_length": 892,
"cds_start": 2162,
"cds_end": null,
"cds_length": 2679,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000858651.1"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX6",
"gene_hgnc_id": 8859,
"hgvs_c": "c.2162C>T",
"hgvs_p": "p.Ala721Val",
"transcript": "ENST00000858652.1",
"protein_id": "ENSP00000528711.1",
"transcript_support_level": null,
"aa_start": 721,
"aa_end": null,
"aa_length": 892,
"cds_start": 2162,
"cds_end": null,
"cds_length": 2679,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000858652.1"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX6",
"gene_hgnc_id": 8859,
"hgvs_c": "c.2108C>T",
"hgvs_p": "p.Ala703Val",
"transcript": "ENST00000970122.1",
"protein_id": "ENSP00000640181.1",
"transcript_support_level": null,
"aa_start": 703,
"aa_end": null,
"aa_length": 874,
"cds_start": 2108,
"cds_end": null,
"cds_length": 2625,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000970122.1"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX6",
"gene_hgnc_id": 8859,
"hgvs_c": "c.2105C>T",
"hgvs_p": "p.Ala702Val",
"transcript": "ENST00000970123.1",
"protein_id": "ENSP00000640182.1",
"transcript_support_level": null,
"aa_start": 702,
"aa_end": null,
"aa_length": 873,
"cds_start": 2105,
"cds_end": null,
"cds_length": 2622,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000970123.1"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX6",
"gene_hgnc_id": 8859,
"hgvs_c": "c.2162C>T",
"hgvs_p": "p.Ala721Val",
"transcript": "ENST00000858657.1",
"protein_id": "ENSP00000528716.1",
"transcript_support_level": null,
"aa_start": 721,
"aa_end": null,
"aa_length": 866,
"cds_start": 2162,
"cds_end": null,
"cds_length": 2601,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000858657.1"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX6",
"gene_hgnc_id": 8859,
"hgvs_c": "c.1868C>T",
"hgvs_p": "p.Ala623Val",
"transcript": "ENST00000970121.1",
"protein_id": "ENSP00000640180.1",
"transcript_support_level": null,
"aa_start": 623,
"aa_end": null,
"aa_length": 794,
"cds_start": 1868,
"cds_end": null,
"cds_length": 2385,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000970121.1"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX6",
"gene_hgnc_id": 8859,
"hgvs_c": "c.1769C>T",
"hgvs_p": "p.Ala590Val",
"transcript": "ENST00000858655.1",
"protein_id": "ENSP00000528714.1",
"transcript_support_level": null,
"aa_start": 590,
"aa_end": null,
"aa_length": 761,
"cds_start": 1769,
"cds_end": null,
"cds_length": 2286,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000858655.1"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX6",
"gene_hgnc_id": 8859,
"hgvs_c": "c.2342C>T",
"hgvs_p": "p.Ala781Val",
"transcript": "XM_011514661.3",
"protein_id": "XP_011512963.1",
"transcript_support_level": null,
"aa_start": 781,
"aa_end": null,
"aa_length": 952,
"cds_start": 2342,
"cds_end": null,
"cds_length": 2859,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011514661.3"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX6",
"gene_hgnc_id": 8859,
"hgvs_c": "c.1286C>T",
"hgvs_p": "p.Ala429Val",
"transcript": "XM_047418872.1",
"protein_id": "XP_047274828.1",
"transcript_support_level": null,
"aa_start": 429,
"aa_end": null,
"aa_length": 600,
"cds_start": 1286,
"cds_end": null,
"cds_length": 1803,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047418872.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX6",
"gene_hgnc_id": 8859,
"hgvs_c": "n.2210C>T",
"hgvs_p": null,
"transcript": "NR_133009.2",
"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": "NR_133009.2"
}
],
"gene_symbol": "PEX6",
"gene_hgnc_id": 8859,
"dbsnp": "rs35830695",
"frequency_reference_population": 0.057302866,
"hom_count_reference_population": 3045,
"allele_count_reference_population": 92467,
"gnomad_exomes_af": 0.0557902,
"gnomad_genomes_af": 0.0718352,
"gnomad_exomes_ac": 81539,
"gnomad_genomes_ac": 10928,
"gnomad_exomes_homalt": 2542,
"gnomad_genomes_homalt": 503,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.004077047109603882,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.07999999821186066,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.603,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.7672,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": -0.06,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 10.003,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.08,
"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": "Benign",
"acmg_criteria": "PM1,BP4_Strong,BP6_Very_Strong,BA1",
"acmg_by_gene": [
{
"score": -18,
"benign_score": 20,
"pathogenic_score": 2,
"criteria": [
"PM1",
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "NM_000287.4",
"gene_symbol": "PEX6",
"hgnc_id": 8859,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2426C>T",
"hgvs_p": "p.Ala809Val"
}
],
"clinvar_disease": "Heimler syndrome 2,Peroxisome biogenesis disorder,Peroxisome biogenesis disorder 4A (Zellweger),Peroxisome biogenesis disorder 4B,Zellweger spectrum disorders,not provided,not specified",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:2 B:9",
"phenotype_combined": "not specified|not provided|Peroxisome biogenesis disorder 4A (Zellweger)|Zellweger spectrum disorders|Heimler syndrome 2|Peroxisome biogenesis disorder|Peroxisome biogenesis disorder 4B",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}