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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: 3-129433246-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=129433246&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 129433246,
"ref": "G",
"alt": "A",
"effect": "splice_region_variant,synonymous_variant",
"transcript": "ENST00000429544.7",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MBD4",
"gene_hgnc_id": 6919,
"hgvs_c": "c.1395C>T",
"hgvs_p": "p.Gly465Gly",
"transcript": "NM_001276270.2",
"protein_id": "NP_001263199.1",
"transcript_support_level": null,
"aa_start": 465,
"aa_end": null,
"aa_length": 574,
"cds_start": 1395,
"cds_end": null,
"cds_length": 1725,
"cdna_start": 1510,
"cdna_end": null,
"cdna_length": 2394,
"mane_select": "ENST00000429544.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MBD4",
"gene_hgnc_id": 6919,
"hgvs_c": "c.1395C>T",
"hgvs_p": "p.Gly465Gly",
"transcript": "ENST00000429544.7",
"protein_id": "ENSP00000394080.2",
"transcript_support_level": 1,
"aa_start": 465,
"aa_end": null,
"aa_length": 574,
"cds_start": 1395,
"cds_end": null,
"cds_length": 1725,
"cdna_start": 1510,
"cdna_end": null,
"cdna_length": 2394,
"mane_select": "NM_001276270.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MBD4",
"gene_hgnc_id": 6919,
"hgvs_c": "c.1413C>T",
"hgvs_p": "p.Gly471Gly",
"transcript": "ENST00000249910.5",
"protein_id": "ENSP00000249910.1",
"transcript_support_level": 1,
"aa_start": 471,
"aa_end": null,
"aa_length": 580,
"cds_start": 1413,
"cds_end": null,
"cds_length": 1743,
"cdna_start": 1589,
"cdna_end": null,
"cdna_length": 2470,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MBD4",
"gene_hgnc_id": 6919,
"hgvs_c": "c.1413C>T",
"hgvs_p": "p.Gly471Gly",
"transcript": "ENST00000503197.5",
"protein_id": "ENSP00000424873.1",
"transcript_support_level": 1,
"aa_start": 471,
"aa_end": null,
"aa_length": 540,
"cds_start": 1413,
"cds_end": null,
"cds_length": 1623,
"cdna_start": 1587,
"cdna_end": null,
"cdna_length": 2099,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MBD4",
"gene_hgnc_id": 6919,
"hgvs_c": "c.459C>T",
"hgvs_p": "p.Gly153Gly",
"transcript": "ENST00000393278.6",
"protein_id": "ENSP00000376959.2",
"transcript_support_level": 1,
"aa_start": 153,
"aa_end": null,
"aa_length": 262,
"cds_start": 459,
"cds_end": null,
"cds_length": 789,
"cdna_start": 805,
"cdna_end": null,
"cdna_length": 1684,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MBD4",
"gene_hgnc_id": 6919,
"hgvs_c": "c.1413C>T",
"hgvs_p": "p.Gly471Gly",
"transcript": "NM_003925.3",
"protein_id": "NP_003916.1",
"transcript_support_level": null,
"aa_start": 471,
"aa_end": null,
"aa_length": 580,
"cds_start": 1413,
"cds_end": null,
"cds_length": 1743,
"cdna_start": 1528,
"cdna_end": null,
"cdna_length": 2412,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MBD4",
"gene_hgnc_id": 6919,
"hgvs_c": "c.1413C>T",
"hgvs_p": "p.Gly471Gly",
"transcript": "NM_001276271.2",
"protein_id": "NP_001263200.1",
"transcript_support_level": null,
"aa_start": 471,
"aa_end": null,
"aa_length": 572,
"cds_start": 1413,
"cds_end": null,
"cds_length": 1719,
"cdna_start": 1528,
"cdna_end": null,
"cdna_length": 2107,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MBD4",
"gene_hgnc_id": 6919,
"hgvs_c": "c.1413C>T",
"hgvs_p": "p.Gly471Gly",
"transcript": "ENST00000507208.1",
"protein_id": "ENSP00000422327.1",
"transcript_support_level": 2,
"aa_start": 471,
"aa_end": null,
"aa_length": 572,
"cds_start": 1413,
"cds_end": null,
"cds_length": 1719,
"cdna_start": 1615,
"cdna_end": null,
"cdna_length": 2194,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MBD4",
"gene_hgnc_id": 6919,
"hgvs_c": "c.1413C>T",
"hgvs_p": "p.Gly471Gly",
"transcript": "NM_001276272.2",
"protein_id": "NP_001263201.1",
"transcript_support_level": null,
"aa_start": 471,
"aa_end": null,
"aa_length": 540,
"cds_start": 1413,
"cds_end": null,
"cds_length": 1623,
"cdna_start": 1528,
"cdna_end": null,
"cdna_length": 2359,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MBD4",
"gene_hgnc_id": 6919,
"hgvs_c": "c.459C>T",
"hgvs_p": "p.Gly153Gly",
"transcript": "NM_001276273.2",
"protein_id": "NP_001263202.1",
"transcript_support_level": null,
"aa_start": 153,
"aa_end": null,
"aa_length": 262,
"cds_start": 459,
"cds_end": null,
"cds_length": 789,
"cdna_start": 574,
"cdna_end": null,
"cdna_length": 1458,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MBD4",
"gene_hgnc_id": 6919,
"hgvs_c": "c.1395C>T",
"hgvs_p": "p.Gly465Gly",
"transcript": "XM_024453810.2",
"protein_id": "XP_024309578.1",
"transcript_support_level": null,
"aa_start": 465,
"aa_end": null,
"aa_length": 566,
"cds_start": 1395,
"cds_end": null,
"cds_length": 1701,
"cdna_start": 1510,
"cdna_end": null,
"cdna_length": 2089,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MBD4",
"gene_hgnc_id": 6919,
"hgvs_c": "c.1395C>T",
"hgvs_p": "p.Gly465Gly",
"transcript": "XM_047449153.1",
"protein_id": "XP_047305109.1",
"transcript_support_level": null,
"aa_start": 465,
"aa_end": null,
"aa_length": 534,
"cds_start": 1395,
"cds_end": null,
"cds_length": 1605,
"cdna_start": 1510,
"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": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MBD4",
"gene_hgnc_id": 6919,
"hgvs_c": "n.106C>T",
"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": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MBD4",
"gene_hgnc_id": 6919,
"hgvs_c": "n.308C>T",
"hgvs_p": null,
"transcript": "ENST00000511009.1",
"protein_id": null,
"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": 530,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MBD4",
"gene_hgnc_id": 6919,
"hgvs_c": "n.256C>T",
"hgvs_p": null,
"transcript": "ENST00000515266.1",
"protein_id": null,
"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": 434,
"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+14G>A",
"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+14G>A",
"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": "rs140696",
"frequency_reference_population": 0.11033982,
"hom_count_reference_population": 11984,
"allele_count_reference_population": 178028,
"gnomad_exomes_af": 0.108106,
"gnomad_genomes_af": 0.131798,
"gnomad_exomes_ac": 157976,
"gnomad_genomes_ac": 20052,
"gnomad_exomes_homalt": 10307,
"gnomad_genomes_homalt": 1677,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.800000011920929,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.0820000022649765,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.8,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -1.225,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.01,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.00000967161446197868,
"dbscsnv_ada_prediction": "Benign",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -21,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BA1",
"acmg_by_gene": [
{
"score": -21,
"benign_score": 21,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000429544.7",
"gene_symbol": "MBD4",
"hgnc_id": 6919,
"effects": [
"splice_region_variant",
"synonymous_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.1395C>T",
"hgvs_p": "p.Gly465Gly"
},
{
"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+14G>A",
"hgvs_p": null
}
],
"clinvar_disease": "Inborn genetic diseases,not provided",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:5",
"phenotype_combined": "not provided|Inborn genetic diseases",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}