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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: 19-35299590-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=35299590&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 35299590,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000392213.8",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MAG",
"gene_hgnc_id": 6783,
"hgvs_c": "c.452C>T",
"hgvs_p": "p.Ala151Val",
"transcript": "NM_002361.4",
"protein_id": "NP_002352.1",
"transcript_support_level": null,
"aa_start": 151,
"aa_end": null,
"aa_length": 626,
"cds_start": 452,
"cds_end": null,
"cds_length": 1881,
"cdna_start": 575,
"cdna_end": null,
"cdna_length": 2357,
"mane_select": "ENST00000392213.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MAG",
"gene_hgnc_id": 6783,
"hgvs_c": "c.452C>T",
"hgvs_p": "p.Ala151Val",
"transcript": "ENST00000392213.8",
"protein_id": "ENSP00000376048.2",
"transcript_support_level": 1,
"aa_start": 151,
"aa_end": null,
"aa_length": 626,
"cds_start": 452,
"cds_end": null,
"cds_length": 1881,
"cdna_start": 575,
"cdna_end": null,
"cdna_length": 2357,
"mane_select": "NM_002361.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MAG",
"gene_hgnc_id": 6783,
"hgvs_c": "c.377C>T",
"hgvs_p": "p.Ala126Val",
"transcript": "ENST00000537831.2",
"protein_id": "ENSP00000440695.1",
"transcript_support_level": 1,
"aa_start": 126,
"aa_end": null,
"aa_length": 601,
"cds_start": 377,
"cds_end": null,
"cds_length": 1806,
"cdna_start": 562,
"cdna_end": null,
"cdna_length": 2341,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MAG",
"gene_hgnc_id": 6783,
"hgvs_c": "c.452C>T",
"hgvs_p": "p.Ala151Val",
"transcript": "ENST00000361922.8",
"protein_id": "ENSP00000355234.4",
"transcript_support_level": 1,
"aa_start": 151,
"aa_end": null,
"aa_length": 582,
"cds_start": 452,
"cds_end": null,
"cds_length": 1749,
"cdna_start": 602,
"cdna_end": null,
"cdna_length": 2426,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MAG",
"gene_hgnc_id": 6783,
"hgvs_c": "c.377C>T",
"hgvs_p": "p.Ala126Val",
"transcript": "NM_001199216.2",
"protein_id": "NP_001186145.1",
"transcript_support_level": null,
"aa_start": 126,
"aa_end": null,
"aa_length": 601,
"cds_start": 377,
"cds_end": null,
"cds_length": 1806,
"cdna_start": 562,
"cdna_end": null,
"cdna_length": 2344,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MAG",
"gene_hgnc_id": 6783,
"hgvs_c": "c.452C>T",
"hgvs_p": "p.Ala151Val",
"transcript": "NM_080600.3",
"protein_id": "NP_542167.1",
"transcript_support_level": null,
"aa_start": 151,
"aa_end": null,
"aa_length": 582,
"cds_start": 452,
"cds_end": null,
"cds_length": 1749,
"cdna_start": 575,
"cdna_end": null,
"cdna_length": 2402,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MAG",
"gene_hgnc_id": 6783,
"hgvs_c": "c.452C>T",
"hgvs_p": "p.Ala151Val",
"transcript": "ENST00000595791.5",
"protein_id": "ENSP00000473125.1",
"transcript_support_level": 4,
"aa_start": 151,
"aa_end": null,
"aa_length": 157,
"cds_start": 452,
"cds_end": null,
"cds_length": 475,
"cdna_start": 562,
"cdna_end": null,
"cdna_length": 585,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MAG",
"gene_hgnc_id": 6783,
"hgvs_c": "c.377C>T",
"hgvs_p": "p.Ala126Val",
"transcript": "ENST00000600291.5",
"protein_id": "ENSP00000470772.1",
"transcript_support_level": 4,
"aa_start": 126,
"aa_end": null,
"aa_length": 130,
"cds_start": 377,
"cds_end": null,
"cds_length": 394,
"cdna_start": 542,
"cdna_end": null,
"cdna_length": 559,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MAG",
"gene_hgnc_id": 6783,
"hgvs_c": "c.*36C>T",
"hgvs_p": null,
"transcript": "ENST00000597035.5",
"protein_id": "ENSP00000473245.1",
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": 58,
"cds_start": -4,
"cds_end": null,
"cds_length": 177,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 542,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "MAG",
"gene_hgnc_id": 6783,
"dbsnp": "rs144553163",
"frequency_reference_population": 0.0053000404,
"hom_count_reference_population": 40,
"allele_count_reference_population": 8495,
"gnomad_exomes_af": 0.00544039,
"gnomad_genomes_af": 0.00396042,
"gnomad_exomes_ac": 7893,
"gnomad_genomes_ac": 602,
"gnomad_exomes_homalt": 37,
"gnomad_genomes_homalt": 3,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.009121209383010864,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.37,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.179,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.24,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.345,
"phylop100way_prediction": "Benign",
"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": -13,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6,BS1,BS2",
"acmg_by_gene": [
{
"score": -13,
"benign_score": 13,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000392213.8",
"gene_symbol": "MAG",
"hgnc_id": 6783,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.452C>T",
"hgvs_p": "p.Ala151Val"
}
],
"clinvar_disease": "Hereditary spastic paraplegia,Hereditary spastic paraplegia 75,MAG-related disorder,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:2 LB:2",
"phenotype_combined": "Hereditary spastic paraplegia|not provided|Hereditary spastic paraplegia 75|MAG-related disorder",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}