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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: 4-3493307-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=3493307&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 3493307,
"ref": "G",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000340083.6",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DOK7",
"gene_hgnc_id": 26594,
"hgvs_c": "c.1321G>C",
"hgvs_p": "p.Gly441Arg",
"transcript": "NM_173660.5",
"protein_id": "NP_775931.3",
"transcript_support_level": null,
"aa_start": 441,
"aa_end": null,
"aa_length": 504,
"cds_start": 1321,
"cds_end": null,
"cds_length": 1515,
"cdna_start": 1391,
"cdna_end": null,
"cdna_length": 2566,
"mane_select": "ENST00000340083.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DOK7",
"gene_hgnc_id": 26594,
"hgvs_c": "c.1321G>C",
"hgvs_p": "p.Gly441Arg",
"transcript": "ENST00000340083.6",
"protein_id": "ENSP00000344432.5",
"transcript_support_level": 1,
"aa_start": 441,
"aa_end": null,
"aa_length": 504,
"cds_start": 1321,
"cds_end": null,
"cds_length": 1515,
"cdna_start": 1391,
"cdna_end": null,
"cdna_length": 2566,
"mane_select": "NM_173660.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DOK7",
"gene_hgnc_id": 26594,
"hgvs_c": "c.1321G>C",
"hgvs_p": "p.Gly441Arg",
"transcript": "NM_001301071.2",
"protein_id": "NP_001288000.1",
"transcript_support_level": null,
"aa_start": 441,
"aa_end": null,
"aa_length": 608,
"cds_start": 1321,
"cds_end": null,
"cds_length": 1827,
"cdna_start": 1391,
"cdna_end": null,
"cdna_length": 2554,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DOK7",
"gene_hgnc_id": 26594,
"hgvs_c": "c.889G>C",
"hgvs_p": "p.Gly297Arg",
"transcript": "NM_001363811.2",
"protein_id": "NP_001350740.1",
"transcript_support_level": null,
"aa_start": 297,
"aa_end": null,
"aa_length": 464,
"cds_start": 889,
"cds_end": null,
"cds_length": 1395,
"cdna_start": 959,
"cdna_end": null,
"cdna_length": 2122,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DOK7",
"gene_hgnc_id": 26594,
"hgvs_c": "c.889G>C",
"hgvs_p": "p.Gly297Arg",
"transcript": "ENST00000643608.1",
"protein_id": "ENSP00000495701.1",
"transcript_support_level": null,
"aa_start": 297,
"aa_end": null,
"aa_length": 464,
"cds_start": 889,
"cds_end": null,
"cds_length": 1395,
"cdna_start": 954,
"cdna_end": null,
"cdna_length": 2108,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DOK7",
"gene_hgnc_id": 26594,
"hgvs_c": "c.391G>C",
"hgvs_p": "p.Gly131Arg",
"transcript": "NM_001256896.2",
"protein_id": "NP_001243825.1",
"transcript_support_level": null,
"aa_start": 131,
"aa_end": null,
"aa_length": 194,
"cds_start": 391,
"cds_end": null,
"cds_length": 585,
"cdna_start": 1089,
"cdna_end": null,
"cdna_length": 2264,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DOK7",
"gene_hgnc_id": 26594,
"hgvs_c": "c.391G>C",
"hgvs_p": "p.Gly131Arg",
"transcript": "ENST00000515886.5",
"protein_id": "ENSP00000492194.1",
"transcript_support_level": 2,
"aa_start": 131,
"aa_end": null,
"aa_length": 194,
"cds_start": 391,
"cds_end": null,
"cds_length": 585,
"cdna_start": 1089,
"cdna_end": null,
"cdna_length": 2263,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DOK7",
"gene_hgnc_id": 26594,
"hgvs_c": "c.1321G>C",
"hgvs_p": "p.Gly441Arg",
"transcript": "XM_011513435.3",
"protein_id": "XP_011511737.1",
"transcript_support_level": null,
"aa_start": 441,
"aa_end": null,
"aa_length": 636,
"cds_start": 1321,
"cds_end": null,
"cds_length": 1911,
"cdna_start": 1391,
"cdna_end": null,
"cdna_length": 2376,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DOK7",
"gene_hgnc_id": 26594,
"hgvs_c": "c.907G>C",
"hgvs_p": "p.Gly303Arg",
"transcript": "XM_047450078.1",
"protein_id": "XP_047306034.1",
"transcript_support_level": null,
"aa_start": 303,
"aa_end": null,
"aa_length": 498,
"cds_start": 907,
"cds_end": null,
"cds_length": 1497,
"cdna_start": 907,
"cdna_end": null,
"cdna_length": 1892,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DOK7",
"gene_hgnc_id": 26594,
"hgvs_c": "c.1075G>C",
"hgvs_p": "p.Gly359Arg",
"transcript": "XM_047450079.1",
"protein_id": "XP_047306035.1",
"transcript_support_level": null,
"aa_start": 359,
"aa_end": null,
"aa_length": 422,
"cds_start": 1075,
"cds_end": null,
"cds_length": 1269,
"cdna_start": 1421,
"cdna_end": null,
"cdna_length": 2596,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DOK7",
"gene_hgnc_id": 26594,
"hgvs_c": "c.391G>C",
"hgvs_p": "p.Gly131Arg",
"transcript": "XM_047450080.1",
"protein_id": "XP_047306036.1",
"transcript_support_level": null,
"aa_start": 131,
"aa_end": null,
"aa_length": 298,
"cds_start": 391,
"cds_end": null,
"cds_length": 897,
"cdna_start": 822,
"cdna_end": null,
"cdna_length": 1985,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DOK7",
"gene_hgnc_id": 26594,
"hgvs_c": "c.391G>C",
"hgvs_p": "p.Gly131Arg",
"transcript": "XM_047450081.1",
"protein_id": "XP_047306037.1",
"transcript_support_level": null,
"aa_start": 131,
"aa_end": null,
"aa_length": 194,
"cds_start": 391,
"cds_end": null,
"cds_length": 585,
"cdna_start": 822,
"cdna_end": null,
"cdna_length": 1997,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DOK7",
"gene_hgnc_id": 26594,
"hgvs_c": "c.*542G>C",
"hgvs_p": null,
"transcript": "NM_001164673.2",
"protein_id": "NP_001158145.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 255,
"cds_start": -4,
"cds_end": null,
"cds_length": 768,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2555,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DOK7",
"gene_hgnc_id": 26594,
"hgvs_c": "c.*542G>C",
"hgvs_p": null,
"transcript": "ENST00000507039.5",
"protein_id": "ENSP00000423614.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 255,
"cds_start": -4,
"cds_end": null,
"cds_length": 768,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2551,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "DOK7",
"gene_hgnc_id": 26594,
"dbsnp": "rs778266118",
"frequency_reference_population": 0.0000037363577,
"hom_count_reference_population": 0,
"allele_count_reference_population": 6,
"gnomad_exomes_af": 0.00000343969,
"gnomad_genomes_af": 0.00000656935,
"gnomad_exomes_ac": 5,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.32205161452293396,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.148,
"revel_prediction": "Benign",
"alphamissense_score": 0.1245,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.27,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 5.606,
"phylop100way_prediction": "Uncertain_significance",
"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": 1,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4",
"acmg_by_gene": [
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000340083.6",
"gene_symbol": "DOK7",
"hgnc_id": 26594,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1321G>C",
"hgvs_p": "p.Gly441Arg"
}
],
"clinvar_disease": "Inborn genetic diseases",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Inborn genetic diseases",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}