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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: 6-42965097-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=42965097&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "6",
"pos": 42965097,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_000287.4",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX6",
"gene_hgnc_id": 8859,
"hgvs_c": "c.2644G>A",
"hgvs_p": "p.Val882Ile",
"transcript": "NM_000287.4",
"protein_id": "NP_000278.3",
"transcript_support_level": null,
"aa_start": 882,
"aa_end": null,
"aa_length": 980,
"cds_start": 2644,
"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": "V",
"aa_alt": "I",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX6",
"gene_hgnc_id": 8859,
"hgvs_c": "c.2644G>A",
"hgvs_p": "p.Val882Ile",
"transcript": "ENST00000304611.13",
"protein_id": "ENSP00000303511.8",
"transcript_support_level": 1,
"aa_start": 882,
"aa_end": null,
"aa_length": 980,
"cds_start": 2644,
"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": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX6",
"gene_hgnc_id": 8859,
"hgvs_c": "c.*180G>A",
"hgvs_p": null,
"transcript": "ENST00000244546.4",
"protein_id": "ENSP00000244546.4",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 738,
"cds_start": null,
"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": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX6",
"gene_hgnc_id": 8859,
"hgvs_c": "c.2683G>A",
"hgvs_p": "p.Val895Ile",
"transcript": "ENST00000858656.1",
"protein_id": "ENSP00000528715.1",
"transcript_support_level": null,
"aa_start": 895,
"aa_end": null,
"aa_length": 993,
"cds_start": 2683,
"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": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX6",
"gene_hgnc_id": 8859,
"hgvs_c": "c.2665G>A",
"hgvs_p": "p.Val889Ile",
"transcript": "ENST00000858658.1",
"protein_id": "ENSP00000528717.1",
"transcript_support_level": null,
"aa_start": 889,
"aa_end": null,
"aa_length": 987,
"cds_start": 2665,
"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": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX6",
"gene_hgnc_id": 8859,
"hgvs_c": "c.2644G>A",
"hgvs_p": "p.Val882Ile",
"transcript": "ENST00000970120.1",
"protein_id": "ENSP00000640179.1",
"transcript_support_level": null,
"aa_start": 882,
"aa_end": null,
"aa_length": 980,
"cds_start": 2644,
"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": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX6",
"gene_hgnc_id": 8859,
"hgvs_c": "c.2560G>A",
"hgvs_p": "p.Val854Ile",
"transcript": "ENST00000858653.1",
"protein_id": "ENSP00000528712.1",
"transcript_support_level": null,
"aa_start": 854,
"aa_end": null,
"aa_length": 952,
"cds_start": 2560,
"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": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX6",
"gene_hgnc_id": 8859,
"hgvs_c": "c.2380G>A",
"hgvs_p": "p.Val794Ile",
"transcript": "NM_001316313.2",
"protein_id": "NP_001303242.1",
"transcript_support_level": null,
"aa_start": 794,
"aa_end": null,
"aa_length": 892,
"cds_start": 2380,
"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": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX6",
"gene_hgnc_id": 8859,
"hgvs_c": "c.2380G>A",
"hgvs_p": "p.Val794Ile",
"transcript": "ENST00000858651.1",
"protein_id": "ENSP00000528710.1",
"transcript_support_level": null,
"aa_start": 794,
"aa_end": null,
"aa_length": 892,
"cds_start": 2380,
"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": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX6",
"gene_hgnc_id": 8859,
"hgvs_c": "c.2380G>A",
"hgvs_p": "p.Val794Ile",
"transcript": "ENST00000858652.1",
"protein_id": "ENSP00000528711.1",
"transcript_support_level": null,
"aa_start": 794,
"aa_end": null,
"aa_length": 892,
"cds_start": 2380,
"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": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX6",
"gene_hgnc_id": 8859,
"hgvs_c": "c.2326G>A",
"hgvs_p": "p.Val776Ile",
"transcript": "ENST00000970122.1",
"protein_id": "ENSP00000640181.1",
"transcript_support_level": null,
"aa_start": 776,
"aa_end": null,
"aa_length": 874,
"cds_start": 2326,
"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": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX6",
"gene_hgnc_id": 8859,
"hgvs_c": "c.2323G>A",
"hgvs_p": "p.Val775Ile",
"transcript": "ENST00000970123.1",
"protein_id": "ENSP00000640182.1",
"transcript_support_level": null,
"aa_start": 775,
"aa_end": null,
"aa_length": 873,
"cds_start": 2323,
"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": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX6",
"gene_hgnc_id": 8859,
"hgvs_c": "c.2086G>A",
"hgvs_p": "p.Val696Ile",
"transcript": "ENST00000970121.1",
"protein_id": "ENSP00000640180.1",
"transcript_support_level": null,
"aa_start": 696,
"aa_end": null,
"aa_length": 794,
"cds_start": 2086,
"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": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX6",
"gene_hgnc_id": 8859,
"hgvs_c": "c.1987G>A",
"hgvs_p": "p.Val663Ile",
"transcript": "ENST00000858655.1",
"protein_id": "ENSP00000528714.1",
"transcript_support_level": null,
"aa_start": 663,
"aa_end": null,
"aa_length": 761,
"cds_start": 1987,
"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": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX6",
"gene_hgnc_id": 8859,
"hgvs_c": "c.2560G>A",
"hgvs_p": "p.Val854Ile",
"transcript": "XM_011514661.3",
"protein_id": "XP_011512963.1",
"transcript_support_level": null,
"aa_start": 854,
"aa_end": null,
"aa_length": 952,
"cds_start": 2560,
"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": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX6",
"gene_hgnc_id": 8859,
"hgvs_c": "c.1504G>A",
"hgvs_p": "p.Val502Ile",
"transcript": "XM_047418872.1",
"protein_id": "XP_047274828.1",
"transcript_support_level": null,
"aa_start": 502,
"aa_end": null,
"aa_length": 600,
"cds_start": 1504,
"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": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": 14,
"intron_rank_end": null,
"gene_symbol": "PEX6",
"gene_hgnc_id": 8859,
"hgvs_c": "c.2588+155G>A",
"hgvs_p": null,
"transcript": "ENST00000858654.1",
"protein_id": "ENSP00000528713.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 954,
"cds_start": null,
"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": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": 14,
"intron_rank_end": null,
"gene_symbol": "PEX6",
"gene_hgnc_id": 8859,
"hgvs_c": "c.2324+155G>A",
"hgvs_p": null,
"transcript": "ENST00000858657.1",
"protein_id": "ENSP00000528716.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 866,
"cds_start": null,
"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": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX6",
"gene_hgnc_id": 8859,
"hgvs_c": "n.2428G>A",
"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": "rs2274516",
"frequency_reference_population": 0.025946356,
"hom_count_reference_population": 641,
"allele_count_reference_population": 41881,
"gnomad_exomes_af": 0.0264628,
"gnomad_genomes_af": 0.0209901,
"gnomad_exomes_ac": 38684,
"gnomad_genomes_ac": 3197,
"gnomad_exomes_homalt": 598,
"gnomad_genomes_homalt": 43,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.009148865938186646,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.289,
"revel_prediction": "Benign",
"alphamissense_score": 0.0951,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.41,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.61,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.02,
"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,BS1,BS2",
"acmg_by_gene": [
{
"score": -18,
"benign_score": 20,
"pathogenic_score": 2,
"criteria": [
"PM1",
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_000287.4",
"gene_symbol": "PEX6",
"hgnc_id": 8859,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2644G>A",
"hgvs_p": "p.Val882Ile"
}
],
"clinvar_disease": "Peroxisome biogenesis disorder,Peroxisome biogenesis disorder 4A (Zellweger),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:4",
"phenotype_combined": "not specified|not provided|Peroxisome biogenesis disorder|Zellweger spectrum disorders|Peroxisome biogenesis disorder 4A (Zellweger)",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}