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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: 17-4899375-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=4899375&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "17",
"pos": 4899375,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_000080.4",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHRNE",
"gene_hgnc_id": 1966,
"hgvs_c": "c.1042G>A",
"hgvs_p": "p.Glu348Lys",
"transcript": "NM_000080.4",
"protein_id": "NP_000071.1",
"transcript_support_level": null,
"aa_start": 348,
"aa_end": null,
"aa_length": 493,
"cds_start": 1042,
"cds_end": null,
"cds_length": 1482,
"cdna_start": 1077,
"cdna_end": null,
"cdna_length": 2482,
"mane_select": "ENST00000649488.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHRNE",
"gene_hgnc_id": 1966,
"hgvs_c": "c.1042G>A",
"hgvs_p": "p.Glu348Lys",
"transcript": "ENST00000649488.2",
"protein_id": "ENSP00000497829.1",
"transcript_support_level": null,
"aa_start": 348,
"aa_end": null,
"aa_length": 493,
"cds_start": 1042,
"cds_end": null,
"cds_length": 1482,
"cdna_start": 1077,
"cdna_end": null,
"cdna_length": 2482,
"mane_select": "NM_000080.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHRNE",
"gene_hgnc_id": 1966,
"hgvs_c": "c.109G>A",
"hgvs_p": "p.Glu37Lys",
"transcript": "ENST00000649830.1",
"protein_id": "ENSP00000496907.1",
"transcript_support_level": null,
"aa_start": 37,
"aa_end": null,
"aa_length": 179,
"cds_start": 109,
"cds_end": null,
"cds_length": 540,
"cdna_start": 1093,
"cdna_end": null,
"cdna_length": 2293,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHRNE",
"gene_hgnc_id": 1966,
"hgvs_c": "c.1006G>A",
"hgvs_p": "p.Glu336Lys",
"transcript": "XM_017024115.2",
"protein_id": "XP_016879604.1",
"transcript_support_level": null,
"aa_start": 336,
"aa_end": null,
"aa_length": 481,
"cds_start": 1006,
"cds_end": null,
"cds_length": 1446,
"cdna_start": 1431,
"cdna_end": null,
"cdna_length": 2836,
"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": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHRNE",
"gene_hgnc_id": 1966,
"hgvs_c": "n.728G>A",
"hgvs_p": null,
"transcript": "ENST00000572438.1",
"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": 1847,
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHRNE",
"gene_hgnc_id": 1966,
"hgvs_c": "n.772G>A",
"hgvs_p": null,
"transcript": "ENST00000652550.1",
"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": 2173,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"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": "C17orf107",
"gene_hgnc_id": 37238,
"hgvs_c": "c.-388C>T",
"hgvs_p": null,
"transcript": "NM_001145536.2",
"protein_id": "NP_001139008.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 190,
"cds_start": -4,
"cds_end": null,
"cds_length": 573,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3201,
"mane_select": "ENST00000381365.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"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": "C17orf107",
"gene_hgnc_id": 37238,
"hgvs_c": "c.-388C>T",
"hgvs_p": null,
"transcript": "ENST00000381365.4",
"protein_id": "ENSP00000370770.3",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 190,
"cds_start": -4,
"cds_end": null,
"cds_length": 573,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3201,
"mane_select": "NM_001145536.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "C17orf107",
"gene_hgnc_id": 37238,
"hgvs_c": "c.-388C>T",
"hgvs_p": null,
"transcript": "ENST00000521575.1",
"protein_id": "ENSP00000429241.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 98,
"cds_start": -4,
"cds_end": null,
"cds_length": 297,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1275,
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "C17orf107",
"gene_hgnc_id": 37238,
"hgvs_c": "n.-161C>T",
"hgvs_p": null,
"transcript": "XR_007065253.1",
"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": 4193,
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "C17orf107",
"gene_hgnc_id": 37238,
"hgvs_c": "n.-161C>T",
"hgvs_p": null,
"transcript": "XR_007065254.1",
"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": 4100,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "CHRNE",
"gene_hgnc_id": 1966,
"dbsnp": "rs757968612",
"frequency_reference_population": 0.00022108658,
"hom_count_reference_population": 0,
"allele_count_reference_population": 339,
"gnomad_exomes_af": 0.0002324,
"gnomad_genomes_af": 0.000118346,
"gnomad_exomes_ac": 321,
"gnomad_genomes_ac": 18,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.46139541268348694,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.03999999910593033,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.418,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.1587,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.22,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.071,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.04,
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 0,
"pathogenic_score": 0,
"criteria": [],
"verdict": "Uncertain_significance",
"transcript": "NM_000080.4",
"gene_symbol": "CHRNE",
"hgnc_id": 1966,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.1042G>A",
"hgvs_p": "p.Glu348Lys"
},
{
"score": 0,
"benign_score": 0,
"pathogenic_score": 0,
"criteria": [],
"verdict": "Uncertain_significance",
"transcript": "NM_001145536.2",
"gene_symbol": "C17orf107",
"hgnc_id": 37238,
"effects": [
"upstream_gene_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.-388C>T",
"hgvs_p": null
}
],
"clinvar_disease": "CHRNE-related disorder,Congenital myasthenic syndrome,Congenital myasthenic syndrome 4A,Congenital myasthenic syndrome 4B,Congenital myasthenic syndrome 4C,Inborn genetic diseases,not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:5",
"phenotype_combined": "not provided|Congenital myasthenic syndrome 4A|Congenital myasthenic syndrome 4A;Congenital myasthenic syndrome 4C;Congenital myasthenic syndrome 4B|Congenital myasthenic syndrome|Inborn genetic diseases|CHRNE-related disorder",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}