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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: 1-44875634-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=44875634&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 44875634,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000360403.7",
"consequences": [
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EIF2B3",
"gene_hgnc_id": 3259,
"hgvs_c": "c.1037T>C",
"hgvs_p": "p.Ile346Thr",
"transcript": "NM_020365.5",
"protein_id": "NP_065098.1",
"transcript_support_level": null,
"aa_start": 346,
"aa_end": null,
"aa_length": 452,
"cds_start": 1037,
"cds_end": null,
"cds_length": 1359,
"cdna_start": 1149,
"cdna_end": null,
"cdna_length": 1900,
"mane_select": "ENST00000360403.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EIF2B3",
"gene_hgnc_id": 3259,
"hgvs_c": "c.1037T>C",
"hgvs_p": "p.Ile346Thr",
"transcript": "ENST00000360403.7",
"protein_id": "ENSP00000353575.2",
"transcript_support_level": 1,
"aa_start": 346,
"aa_end": null,
"aa_length": 452,
"cds_start": 1037,
"cds_end": null,
"cds_length": 1359,
"cdna_start": 1149,
"cdna_end": null,
"cdna_length": 1900,
"mane_select": "NM_020365.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EIF2B3",
"gene_hgnc_id": 3259,
"hgvs_c": "c.1037T>C",
"hgvs_p": "p.Ile346Thr",
"transcript": "ENST00000372183.7",
"protein_id": "ENSP00000361257.3",
"transcript_support_level": 1,
"aa_start": 346,
"aa_end": null,
"aa_length": 412,
"cds_start": 1037,
"cds_end": null,
"cds_length": 1239,
"cdna_start": 1141,
"cdna_end": null,
"cdna_length": 1457,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EIF2B3",
"gene_hgnc_id": 3259,
"hgvs_c": "c.1037T>C",
"hgvs_p": "p.Ile346Thr",
"transcript": "ENST00000620860.4",
"protein_id": "ENSP00000483996.1",
"transcript_support_level": 1,
"aa_start": 346,
"aa_end": null,
"aa_length": 401,
"cds_start": 1037,
"cds_end": null,
"cds_length": 1206,
"cdna_start": 1276,
"cdna_end": null,
"cdna_length": 1923,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EIF2B3",
"gene_hgnc_id": 3259,
"hgvs_c": "c.1037T>C",
"hgvs_p": "p.Ile346Thr",
"transcript": "NM_001166588.3",
"protein_id": "NP_001160060.1",
"transcript_support_level": null,
"aa_start": 346,
"aa_end": null,
"aa_length": 412,
"cds_start": 1037,
"cds_end": null,
"cds_length": 1239,
"cdna_start": 1149,
"cdna_end": null,
"cdna_length": 1465,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EIF2B3",
"gene_hgnc_id": 3259,
"hgvs_c": "c.1037T>C",
"hgvs_p": "p.Ile346Thr",
"transcript": "NM_001261418.2",
"protein_id": "NP_001248347.1",
"transcript_support_level": null,
"aa_start": 346,
"aa_end": null,
"aa_length": 401,
"cds_start": 1037,
"cds_end": null,
"cds_length": 1206,
"cdna_start": 1149,
"cdna_end": null,
"cdna_length": 1796,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EIF2B3",
"gene_hgnc_id": 3259,
"hgvs_c": "c.497T>C",
"hgvs_p": "p.Ile166Thr",
"transcript": "ENST00000439363.5",
"protein_id": "ENSP00000396985.1",
"transcript_support_level": 3,
"aa_start": 166,
"aa_end": null,
"aa_length": 221,
"cds_start": 497,
"cds_end": null,
"cds_length": 666,
"cdna_start": 499,
"cdna_end": null,
"cdna_length": 892,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EIF2B3",
"gene_hgnc_id": 3259,
"hgvs_c": "c.947T>C",
"hgvs_p": "p.Ile316Thr",
"transcript": "XM_047433499.1",
"protein_id": "XP_047289455.1",
"transcript_support_level": null,
"aa_start": 316,
"aa_end": null,
"aa_length": 422,
"cds_start": 947,
"cds_end": null,
"cds_length": 1269,
"cdna_start": 1059,
"cdna_end": null,
"cdna_length": 1810,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EIF2B3",
"gene_hgnc_id": 3259,
"hgvs_c": "c.947T>C",
"hgvs_p": "p.Ile316Thr",
"transcript": "XM_047433500.1",
"protein_id": "XP_047289456.1",
"transcript_support_level": null,
"aa_start": 316,
"aa_end": null,
"aa_length": 371,
"cds_start": 947,
"cds_end": null,
"cds_length": 1116,
"cdna_start": 1059,
"cdna_end": null,
"cdna_length": 1706,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EIF2B3",
"gene_hgnc_id": 3259,
"hgvs_c": "c.650T>C",
"hgvs_p": "p.Ile217Thr",
"transcript": "XM_047433501.1",
"protein_id": "XP_047289457.1",
"transcript_support_level": null,
"aa_start": 217,
"aa_end": null,
"aa_length": 323,
"cds_start": 650,
"cds_end": null,
"cds_length": 972,
"cdna_start": 797,
"cdna_end": null,
"cdna_length": 1548,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EIF2B3",
"gene_hgnc_id": 3259,
"hgvs_c": "n.-12T>C",
"hgvs_p": null,
"transcript": "ENST00000486491.1",
"protein_id": null,
"transcript_support_level": 5,
"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": 312,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "EIF2B3",
"gene_hgnc_id": 3259,
"dbsnp": "rs119474039",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9492602348327637,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.684,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.1246,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.44,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 6.658,
"phylop100way_prediction": "Uncertain_significance",
"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": 14,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM2,PP3_Strong,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 14,
"benign_score": 0,
"pathogenic_score": 14,
"criteria": [
"PM2",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000360403.7",
"gene_symbol": "EIF2B3",
"hgnc_id": 3259,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1037T>C",
"hgvs_p": "p.Ile346Thr"
}
],
"clinvar_disease": "Leukoencephalopathy with vanishing white matter 3,Vanishing white matter disease,not provided",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:2 O:1",
"phenotype_combined": "Vanishing white matter disease|Leukoencephalopathy with vanishing white matter 3|not provided",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}