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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: 7-76058047-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=7&pos=76058047&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "7",
"pos": 76058047,
"ref": "C",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000315758.10",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MDH2",
"gene_hgnc_id": 6971,
"hgvs_c": "c.398C>G",
"hgvs_p": "p.Pro133Arg",
"transcript": "NM_005918.4",
"protein_id": "NP_005909.2",
"transcript_support_level": null,
"aa_start": 133,
"aa_end": null,
"aa_length": 338,
"cds_start": 398,
"cds_end": null,
"cds_length": 1017,
"cdna_start": 453,
"cdna_end": null,
"cdna_length": 2170,
"mane_select": "ENST00000315758.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MDH2",
"gene_hgnc_id": 6971,
"hgvs_c": "c.398C>G",
"hgvs_p": "p.Pro133Arg",
"transcript": "ENST00000315758.10",
"protein_id": "ENSP00000327070.5",
"transcript_support_level": 1,
"aa_start": 133,
"aa_end": null,
"aa_length": 338,
"cds_start": 398,
"cds_end": null,
"cds_length": 1017,
"cdna_start": 453,
"cdna_end": null,
"cdna_length": 2170,
"mane_select": "NM_005918.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MDH2",
"gene_hgnc_id": 6971,
"hgvs_c": "c.398C>G",
"hgvs_p": "p.Pro133Arg",
"transcript": "NM_001282403.2",
"protein_id": "NP_001269332.1",
"transcript_support_level": null,
"aa_start": 133,
"aa_end": null,
"aa_length": 296,
"cds_start": 398,
"cds_end": null,
"cds_length": 891,
"cdna_start": 453,
"cdna_end": null,
"cdna_length": 2044,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MDH2",
"gene_hgnc_id": 6971,
"hgvs_c": "c.398C>G",
"hgvs_p": "p.Pro133Arg",
"transcript": "ENST00000432020.2",
"protein_id": "ENSP00000408649.2",
"transcript_support_level": 2,
"aa_start": 133,
"aa_end": null,
"aa_length": 296,
"cds_start": 398,
"cds_end": null,
"cds_length": 891,
"cdna_start": 398,
"cdna_end": null,
"cdna_length": 1548,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MDH2",
"gene_hgnc_id": 6971,
"hgvs_c": "c.77C>G",
"hgvs_p": "p.Pro26Arg",
"transcript": "NM_001282404.2",
"protein_id": "NP_001269333.1",
"transcript_support_level": null,
"aa_start": 26,
"aa_end": null,
"aa_length": 231,
"cds_start": 77,
"cds_end": null,
"cds_length": 696,
"cdna_start": 284,
"cdna_end": null,
"cdna_length": 2001,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MDH2",
"gene_hgnc_id": 6971,
"hgvs_c": "c.77C>G",
"hgvs_p": "p.Pro26Arg",
"transcript": "ENST00000443006.5",
"protein_id": "ENSP00000416929.1",
"transcript_support_level": 2,
"aa_start": 26,
"aa_end": null,
"aa_length": 231,
"cds_start": 77,
"cds_end": null,
"cds_length": 696,
"cdna_start": 305,
"cdna_end": null,
"cdna_length": 2020,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MDH2",
"gene_hgnc_id": 6971,
"hgvs_c": "n.423C>G",
"hgvs_p": null,
"transcript": "ENST00000461665.5",
"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": 551,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "MDH2",
"gene_hgnc_id": 6971,
"dbsnp": "rs375002796",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": 0,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 0,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9723405838012695,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.616,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.5647,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.4,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.324,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0,
"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": 8,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PM5,PP3_Strong",
"acmg_by_gene": [
{
"score": 8,
"benign_score": 0,
"pathogenic_score": 8,
"criteria": [
"PM2",
"PM5",
"PP3_Strong"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000315758.10",
"gene_symbol": "MDH2",
"hgnc_id": 6971,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.398C>G",
"hgvs_p": "p.Pro133Arg"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}