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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: 3-129436620-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=129436620&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 129436620,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000429544.7",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MBD4",
"gene_hgnc_id": 6919,
"hgvs_c": "c.1024T>C",
"hgvs_p": "p.Ser342Pro",
"transcript": "NM_001276270.2",
"protein_id": "NP_001263199.1",
"transcript_support_level": null,
"aa_start": 342,
"aa_end": null,
"aa_length": 574,
"cds_start": 1024,
"cds_end": null,
"cds_length": 1725,
"cdna_start": 1139,
"cdna_end": null,
"cdna_length": 2394,
"mane_select": "ENST00000429544.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "P",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MBD4",
"gene_hgnc_id": 6919,
"hgvs_c": "c.1024T>C",
"hgvs_p": "p.Ser342Pro",
"transcript": "ENST00000429544.7",
"protein_id": "ENSP00000394080.2",
"transcript_support_level": 1,
"aa_start": 342,
"aa_end": null,
"aa_length": 574,
"cds_start": 1024,
"cds_end": null,
"cds_length": 1725,
"cdna_start": 1139,
"cdna_end": null,
"cdna_length": 2394,
"mane_select": "NM_001276270.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MBD4",
"gene_hgnc_id": 6919,
"hgvs_c": "c.1024T>C",
"hgvs_p": "p.Ser342Pro",
"transcript": "ENST00000249910.5",
"protein_id": "ENSP00000249910.1",
"transcript_support_level": 1,
"aa_start": 342,
"aa_end": null,
"aa_length": 580,
"cds_start": 1024,
"cds_end": null,
"cds_length": 1743,
"cdna_start": 1200,
"cdna_end": null,
"cdna_length": 2470,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MBD4",
"gene_hgnc_id": 6919,
"hgvs_c": "c.1024T>C",
"hgvs_p": "p.Ser342Pro",
"transcript": "ENST00000503197.5",
"protein_id": "ENSP00000424873.1",
"transcript_support_level": 1,
"aa_start": 342,
"aa_end": null,
"aa_length": 540,
"cds_start": 1024,
"cds_end": null,
"cds_length": 1623,
"cdna_start": 1198,
"cdna_end": null,
"cdna_length": 2099,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 7,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "MBD4",
"gene_hgnc_id": 6919,
"hgvs_c": "c.247+1188T>C",
"hgvs_p": null,
"transcript": "ENST00000393278.6",
"protein_id": "ENSP00000376959.2",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 262,
"cds_start": -4,
"cds_end": null,
"cds_length": 789,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1684,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MBD4",
"gene_hgnc_id": 6919,
"hgvs_c": "c.1024T>C",
"hgvs_p": "p.Ser342Pro",
"transcript": "NM_003925.3",
"protein_id": "NP_003916.1",
"transcript_support_level": null,
"aa_start": 342,
"aa_end": null,
"aa_length": 580,
"cds_start": 1024,
"cds_end": null,
"cds_length": 1743,
"cdna_start": 1139,
"cdna_end": null,
"cdna_length": 2412,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MBD4",
"gene_hgnc_id": 6919,
"hgvs_c": "c.1024T>C",
"hgvs_p": "p.Ser342Pro",
"transcript": "NM_001276271.2",
"protein_id": "NP_001263200.1",
"transcript_support_level": null,
"aa_start": 342,
"aa_end": null,
"aa_length": 572,
"cds_start": 1024,
"cds_end": null,
"cds_length": 1719,
"cdna_start": 1139,
"cdna_end": null,
"cdna_length": 2107,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MBD4",
"gene_hgnc_id": 6919,
"hgvs_c": "c.1024T>C",
"hgvs_p": "p.Ser342Pro",
"transcript": "ENST00000507208.1",
"protein_id": "ENSP00000422327.1",
"transcript_support_level": 2,
"aa_start": 342,
"aa_end": null,
"aa_length": 572,
"cds_start": 1024,
"cds_end": null,
"cds_length": 1719,
"cdna_start": 1226,
"cdna_end": null,
"cdna_length": 2194,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MBD4",
"gene_hgnc_id": 6919,
"hgvs_c": "c.1024T>C",
"hgvs_p": "p.Ser342Pro",
"transcript": "NM_001276272.2",
"protein_id": "NP_001263201.1",
"transcript_support_level": null,
"aa_start": 342,
"aa_end": null,
"aa_length": 540,
"cds_start": 1024,
"cds_end": null,
"cds_length": 1623,
"cdna_start": 1139,
"cdna_end": null,
"cdna_length": 2359,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MBD4",
"gene_hgnc_id": 6919,
"hgvs_c": "c.1024T>C",
"hgvs_p": "p.Ser342Pro",
"transcript": "XM_024453810.2",
"protein_id": "XP_024309578.1",
"transcript_support_level": null,
"aa_start": 342,
"aa_end": null,
"aa_length": 566,
"cds_start": 1024,
"cds_end": null,
"cds_length": 1701,
"cdna_start": 1139,
"cdna_end": null,
"cdna_length": 2089,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MBD4",
"gene_hgnc_id": 6919,
"hgvs_c": "c.1024T>C",
"hgvs_p": "p.Ser342Pro",
"transcript": "XM_047449153.1",
"protein_id": "XP_047305109.1",
"transcript_support_level": null,
"aa_start": 342,
"aa_end": null,
"aa_length": 534,
"cds_start": 1024,
"cds_end": null,
"cds_length": 1605,
"cdna_start": 1139,
"cdna_end": null,
"cdna_length": 2341,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 7,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "MBD4",
"gene_hgnc_id": 6919,
"hgvs_c": "c.247+1188T>C",
"hgvs_p": null,
"transcript": "NM_001276273.2",
"protein_id": "NP_001263202.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 262,
"cds_start": -4,
"cds_end": null,
"cds_length": 789,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1458,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "MBD4",
"gene_hgnc_id": 6919,
"hgvs_c": "n.442+1100T>C",
"hgvs_p": null,
"transcript": "ENST00000509587.1",
"protein_id": null,
"transcript_support_level": 3,
"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": 643,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "MBD4",
"gene_hgnc_id": 6919,
"hgvs_c": "n.104+3110T>C",
"hgvs_p": null,
"transcript": "ENST00000509828.1",
"protein_id": "ENSP00000422690.1",
"transcript_support_level": 2,
"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": 576,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "IFT122",
"gene_hgnc_id": 13556,
"hgvs_c": "n.288+3388A>G",
"hgvs_p": null,
"transcript": "ENST00000687461.1",
"protein_id": null,
"transcript_support_level": null,
"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": 4333,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "IFT122",
"gene_hgnc_id": 13556,
"hgvs_c": "n.355+3388A>G",
"hgvs_p": null,
"transcript": "ENST00000693654.1",
"protein_id": null,
"transcript_support_level": null,
"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": 4208,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "MBD4",
"gene_hgnc_id": 6919,
"dbsnp": "rs2307289",
"frequency_reference_population": 0.014657521,
"hom_count_reference_population": 1294,
"allele_count_reference_population": 23658,
"gnomad_exomes_af": 0.0119386,
"gnomad_genomes_af": 0.0407662,
"gnomad_exomes_ac": 17452,
"gnomad_genomes_ac": 6206,
"gnomad_exomes_homalt": 914,
"gnomad_genomes_homalt": 380,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.0016411840915679932,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.029999999329447746,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.285,
"revel_prediction": "Benign",
"alphamissense_score": 0.0836,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.44,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.217,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.03,
"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": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BA1",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000429544.7",
"gene_symbol": "MBD4",
"hgnc_id": 6919,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.1024T>C",
"hgvs_p": "p.Ser342Pro"
},
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000687461.1",
"gene_symbol": "IFT122",
"hgnc_id": 13556,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "n.288+3388A>G",
"hgvs_p": null
}
],
"clinvar_disease": "MBD4-related disorder,not provided",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:4",
"phenotype_combined": "not provided|MBD4-related disorder",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}