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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: 4-147638713-A-AT (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=147638713&ref=A&alt=AT&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 147638713,
"ref": "A",
"alt": "AT",
"effect": "frameshift_variant",
"transcript": "NM_138364.4",
"consequences": [
{
"aa_ref": "I",
"aa_alt": "N?",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRMT9",
"gene_hgnc_id": 25099,
"hgvs_c": "c.2356dupA",
"hgvs_p": "p.Ile786fs",
"transcript": "NM_138364.4",
"protein_id": "NP_612373.2",
"transcript_support_level": null,
"aa_start": 786,
"aa_end": null,
"aa_length": 845,
"cds_start": 2356,
"cds_end": null,
"cds_length": 2538,
"cdna_start": 2532,
"cdna_end": null,
"cdna_length": 3461,
"mane_select": "ENST00000322396.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "N?",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRMT9",
"gene_hgnc_id": 25099,
"hgvs_c": "c.2356dupA",
"hgvs_p": "p.Ile786fs",
"transcript": "ENST00000322396.7",
"protein_id": "ENSP00000314396.6",
"transcript_support_level": 1,
"aa_start": 786,
"aa_end": null,
"aa_length": 845,
"cds_start": 2356,
"cds_end": null,
"cds_length": 2538,
"cdna_start": 2532,
"cdna_end": null,
"cdna_length": 3461,
"mane_select": "NM_138364.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "TMEM184C",
"gene_hgnc_id": 25587,
"hgvs_c": "c.779+7209dupT",
"hgvs_p": null,
"transcript": "ENST00000508208.5",
"protein_id": "ENSP00000425940.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 261,
"cds_start": -4,
"cds_end": null,
"cds_length": 786,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1528,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "N?",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRMT9",
"gene_hgnc_id": 25099,
"hgvs_c": "c.2017dupA",
"hgvs_p": "p.Ile673fs",
"transcript": "NM_001304458.2",
"protein_id": "NP_001291387.1",
"transcript_support_level": null,
"aa_start": 673,
"aa_end": null,
"aa_length": 732,
"cds_start": 2017,
"cds_end": null,
"cds_length": 2199,
"cdna_start": 2383,
"cdna_end": null,
"cdna_length": 3312,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "N?",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRMT9",
"gene_hgnc_id": 25099,
"hgvs_c": "c.2017dupA",
"hgvs_p": "p.Ile673fs",
"transcript": "NM_001350142.2",
"protein_id": "NP_001337071.1",
"transcript_support_level": null,
"aa_start": 673,
"aa_end": null,
"aa_length": 732,
"cds_start": 2017,
"cds_end": null,
"cds_length": 2199,
"cdna_start": 2667,
"cdna_end": null,
"cdna_length": 3596,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "N?",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRMT9",
"gene_hgnc_id": 25099,
"hgvs_c": "c.1441dupA",
"hgvs_p": "p.Ile481fs",
"transcript": "NM_001350143.2",
"protein_id": "NP_001337072.1",
"transcript_support_level": null,
"aa_start": 481,
"aa_end": null,
"aa_length": 540,
"cds_start": 1441,
"cds_end": null,
"cds_length": 1623,
"cdna_start": 2111,
"cdna_end": null,
"cdna_length": 3040,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "N?",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRMT9",
"gene_hgnc_id": 25099,
"hgvs_c": "c.1288dupA",
"hgvs_p": "p.Ile430fs",
"transcript": "NM_001350141.2",
"protein_id": "NP_001337070.1",
"transcript_support_level": null,
"aa_start": 430,
"aa_end": null,
"aa_length": 489,
"cds_start": 1288,
"cds_end": null,
"cds_length": 1470,
"cdna_start": 2729,
"cdna_end": null,
"cdna_length": 3658,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "N?",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRMT9",
"gene_hgnc_id": 25099,
"hgvs_c": "c.1132dupA",
"hgvs_p": "p.Ile378fs",
"transcript": "NM_001350144.2",
"protein_id": "NP_001337073.1",
"transcript_support_level": null,
"aa_start": 378,
"aa_end": null,
"aa_length": 437,
"cds_start": 1132,
"cds_end": null,
"cds_length": 1314,
"cdna_start": 2378,
"cdna_end": null,
"cdna_length": 3307,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "N?",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRMT9",
"gene_hgnc_id": 25099,
"hgvs_c": "c.1441dupA",
"hgvs_p": "p.Ile481fs",
"transcript": "XM_047416393.1",
"protein_id": "XP_047272349.1",
"transcript_support_level": null,
"aa_start": 481,
"aa_end": null,
"aa_length": 540,
"cds_start": 1441,
"cds_end": null,
"cds_length": 1623,
"cdna_start": 1678,
"cdna_end": null,
"cdna_length": 2607,
"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": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRMT9",
"gene_hgnc_id": 25099,
"hgvs_c": "n.1683dupA",
"hgvs_p": null,
"transcript": "ENST00000510269.5",
"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": 2012,
"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": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRMT9",
"gene_hgnc_id": 25099,
"hgvs_c": "n.368dupA",
"hgvs_p": null,
"transcript": "ENST00000511687.1",
"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": 401,
"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": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRMT9",
"gene_hgnc_id": 25099,
"hgvs_c": "n.*2006dupA",
"hgvs_p": null,
"transcript": "ENST00000514886.1",
"protein_id": "ENSP00000426732.1",
"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": 2674,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRMT9",
"gene_hgnc_id": 25099,
"hgvs_c": "n.*2006dupA",
"hgvs_p": null,
"transcript": "ENST00000514886.1",
"protein_id": "ENSP00000426732.1",
"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": 2674,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PRMT9",
"gene_hgnc_id": 25099,
"dbsnp": null,
"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": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 1.322,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.01,
"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": 6,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PVS1_Moderate,PM2,PP5_Moderate",
"acmg_by_gene": [
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PVS1_Moderate",
"PM2",
"PP5_Moderate"
],
"verdict": "Likely_pathogenic",
"transcript": "NM_138364.4",
"gene_symbol": "PRMT9",
"hgnc_id": 25099,
"effects": [
"frameshift_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2356dupA",
"hgvs_p": "p.Ile786fs"
},
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP5_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000508208.5",
"gene_symbol": "TMEM184C",
"hgnc_id": 25587,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.779+7209dupT",
"hgvs_p": null
}
],
"clinvar_disease": "Neurodevelopmental abnormality",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "P:1",
"phenotype_combined": "Neurodevelopmental abnormality",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}