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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: 6-42966044-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=42966044&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "6",
"pos": 42966044,
"ref": "C",
"alt": "T",
"effect": "missense_variant,splice_region_variant",
"transcript": "NM_000287.4",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX6",
"gene_hgnc_id": 8859,
"hgvs_c": "c.2362G>A",
"hgvs_p": "p.Val788Met",
"transcript": "NM_000287.4",
"protein_id": "NP_000278.3",
"transcript_support_level": null,
"aa_start": 788,
"aa_end": null,
"aa_length": 980,
"cds_start": 2362,
"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": "M",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX6",
"gene_hgnc_id": 8859,
"hgvs_c": "c.2362G>A",
"hgvs_p": "p.Val788Met",
"transcript": "ENST00000304611.13",
"protein_id": "ENSP00000303511.8",
"transcript_support_level": 1,
"aa_start": 788,
"aa_end": null,
"aa_length": 980,
"cds_start": 2362,
"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": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": 10,
"intron_rank_end": null,
"gene_symbol": "PEX6",
"gene_hgnc_id": 8859,
"hgvs_c": "c.2116-255G>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": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX6",
"gene_hgnc_id": 8859,
"hgvs_c": "c.2362G>A",
"hgvs_p": "p.Ala788Thr",
"transcript": "ENST00000858656.1",
"protein_id": "ENSP00000528715.1",
"transcript_support_level": null,
"aa_start": 788,
"aa_end": null,
"aa_length": 993,
"cds_start": 2362,
"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": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX6",
"gene_hgnc_id": 8859,
"hgvs_c": "c.2383G>A",
"hgvs_p": "p.Val795Met",
"transcript": "ENST00000858658.1",
"protein_id": "ENSP00000528717.1",
"transcript_support_level": null,
"aa_start": 795,
"aa_end": null,
"aa_length": 987,
"cds_start": 2383,
"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": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX6",
"gene_hgnc_id": 8859,
"hgvs_c": "c.2362G>A",
"hgvs_p": "p.Val788Met",
"transcript": "ENST00000970120.1",
"protein_id": "ENSP00000640179.1",
"transcript_support_level": null,
"aa_start": 788,
"aa_end": null,
"aa_length": 980,
"cds_start": 2362,
"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": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_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.2362G>A",
"hgvs_p": "p.Val788Met",
"transcript": "ENST00000858654.1",
"protein_id": "ENSP00000528713.1",
"transcript_support_level": null,
"aa_start": 788,
"aa_end": null,
"aa_length": 954,
"cds_start": 2362,
"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": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX6",
"gene_hgnc_id": 8859,
"hgvs_c": "c.2278G>A",
"hgvs_p": "p.Val760Met",
"transcript": "ENST00000858653.1",
"protein_id": "ENSP00000528712.1",
"transcript_support_level": null,
"aa_start": 760,
"aa_end": null,
"aa_length": 952,
"cds_start": 2278,
"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": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX6",
"gene_hgnc_id": 8859,
"hgvs_c": "c.2098G>A",
"hgvs_p": "p.Val700Met",
"transcript": "NM_001316313.2",
"protein_id": "NP_001303242.1",
"transcript_support_level": null,
"aa_start": 700,
"aa_end": null,
"aa_length": 892,
"cds_start": 2098,
"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": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX6",
"gene_hgnc_id": 8859,
"hgvs_c": "c.2098G>A",
"hgvs_p": "p.Val700Met",
"transcript": "ENST00000858651.1",
"protein_id": "ENSP00000528710.1",
"transcript_support_level": null,
"aa_start": 700,
"aa_end": null,
"aa_length": 892,
"cds_start": 2098,
"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": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX6",
"gene_hgnc_id": 8859,
"hgvs_c": "c.2098G>A",
"hgvs_p": "p.Val700Met",
"transcript": "ENST00000858652.1",
"protein_id": "ENSP00000528711.1",
"transcript_support_level": null,
"aa_start": 700,
"aa_end": null,
"aa_length": 892,
"cds_start": 2098,
"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": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX6",
"gene_hgnc_id": 8859,
"hgvs_c": "c.2044G>A",
"hgvs_p": "p.Val682Met",
"transcript": "ENST00000970122.1",
"protein_id": "ENSP00000640181.1",
"transcript_support_level": null,
"aa_start": 682,
"aa_end": null,
"aa_length": 874,
"cds_start": 2044,
"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": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX6",
"gene_hgnc_id": 8859,
"hgvs_c": "c.2041G>A",
"hgvs_p": "p.Val681Met",
"transcript": "ENST00000970123.1",
"protein_id": "ENSP00000640182.1",
"transcript_support_level": null,
"aa_start": 681,
"aa_end": null,
"aa_length": 873,
"cds_start": 2041,
"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": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_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.2098G>A",
"hgvs_p": "p.Val700Met",
"transcript": "ENST00000858657.1",
"protein_id": "ENSP00000528716.1",
"transcript_support_level": null,
"aa_start": 700,
"aa_end": null,
"aa_length": 866,
"cds_start": 2098,
"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": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX6",
"gene_hgnc_id": 8859,
"hgvs_c": "c.1804G>A",
"hgvs_p": "p.Val602Met",
"transcript": "ENST00000970121.1",
"protein_id": "ENSP00000640180.1",
"transcript_support_level": null,
"aa_start": 602,
"aa_end": null,
"aa_length": 794,
"cds_start": 1804,
"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": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX6",
"gene_hgnc_id": 8859,
"hgvs_c": "c.1705G>A",
"hgvs_p": "p.Val569Met",
"transcript": "ENST00000858655.1",
"protein_id": "ENSP00000528714.1",
"transcript_support_level": null,
"aa_start": 569,
"aa_end": null,
"aa_length": 761,
"cds_start": 1705,
"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": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX6",
"gene_hgnc_id": 8859,
"hgvs_c": "c.2278G>A",
"hgvs_p": "p.Val760Met",
"transcript": "XM_011514661.3",
"protein_id": "XP_011512963.1",
"transcript_support_level": null,
"aa_start": 760,
"aa_end": null,
"aa_length": 952,
"cds_start": 2278,
"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": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX6",
"gene_hgnc_id": 8859,
"hgvs_c": "c.1222G>A",
"hgvs_p": "p.Val408Met",
"transcript": "XM_047418872.1",
"protein_id": "XP_047274828.1",
"transcript_support_level": null,
"aa_start": 408,
"aa_end": null,
"aa_length": 600,
"cds_start": 1222,
"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": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": 10,
"intron_rank_end": null,
"gene_symbol": "PEX6",
"gene_hgnc_id": 8859,
"hgvs_c": "n.2147-255G>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": "rs267608240",
"frequency_reference_population": 0.000007435663,
"hom_count_reference_population": 0,
"allele_count_reference_population": 12,
"gnomad_exomes_af": 0.00000752573,
"gnomad_genomes_af": 0.00000657065,
"gnomad_exomes_ac": 11,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9327014684677124,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.984000027179718,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": 0.921,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.6161,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.48,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.677,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.76,
"spliceai_max_prediction": "Pathogenic",
"dbscsnv_ada_score": 0.999913255837728,
"dbscsnv_ada_prediction": "Pathogenic",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 9,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PS3,PM2,PP3_Moderate,PP5",
"acmg_by_gene": [
{
"score": 9,
"benign_score": 0,
"pathogenic_score": 9,
"criteria": [
"PS3",
"PM2",
"PP3_Moderate",
"PP5"
],
"verdict": "Likely_pathogenic",
"transcript": "NM_000287.4",
"gene_symbol": "PEX6",
"hgnc_id": 8859,
"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2362G>A",
"hgvs_p": "p.Val788Met"
}
],
"clinvar_disease": "Heimler syndrome 2,Peroxisome biogenesis disorder,Peroxisome biogenesis disorder 4A (Zellweger),Peroxisome biogenesis disorder 4B,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "P:5 US:1",
"phenotype_combined": "Peroxisome biogenesis disorder 4A (Zellweger);Peroxisome biogenesis disorder 4B|Peroxisome biogenesis disorder|not provided|Heimler syndrome 2|Peroxisome biogenesis disorder 4A (Zellweger)",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}