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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: 19-6429768-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=6429768&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 6429768,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000321510.7",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC25A41",
"gene_hgnc_id": 28533,
"hgvs_c": "c.580T>C",
"hgvs_p": "p.Ser194Pro",
"transcript": "NM_173637.4",
"protein_id": "NP_775908.2",
"transcript_support_level": null,
"aa_start": 194,
"aa_end": null,
"aa_length": 370,
"cds_start": 580,
"cds_end": null,
"cds_length": 1113,
"cdna_start": 650,
"cdna_end": null,
"cdna_length": 1535,
"mane_select": "ENST00000321510.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "P",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC25A41",
"gene_hgnc_id": 28533,
"hgvs_c": "c.580T>C",
"hgvs_p": "p.Ser194Pro",
"transcript": "ENST00000321510.7",
"protein_id": "ENSP00000322649.5",
"transcript_support_level": 5,
"aa_start": 194,
"aa_end": null,
"aa_length": 370,
"cds_start": 580,
"cds_end": null,
"cds_length": 1113,
"cdna_start": 650,
"cdna_end": null,
"cdna_length": 1535,
"mane_select": "NM_173637.4",
"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": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC25A41",
"gene_hgnc_id": 28533,
"hgvs_c": "n.580T>C",
"hgvs_p": null,
"transcript": "ENST00000597558.5",
"protein_id": "ENSP00000471238.1",
"transcript_support_level": 1,
"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": 1405,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC25A41",
"gene_hgnc_id": 28533,
"hgvs_c": "c.166T>C",
"hgvs_p": "p.Ser56Pro",
"transcript": "NM_001321298.2",
"protein_id": "NP_001308227.1",
"transcript_support_level": null,
"aa_start": 56,
"aa_end": null,
"aa_length": 232,
"cds_start": 166,
"cds_end": null,
"cds_length": 699,
"cdna_start": 748,
"cdna_end": null,
"cdna_length": 1633,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC25A41",
"gene_hgnc_id": 28533,
"hgvs_c": "c.388T>C",
"hgvs_p": "p.Ser130Pro",
"transcript": "XM_011527926.1",
"protein_id": "XP_011526228.1",
"transcript_support_level": null,
"aa_start": 130,
"aa_end": null,
"aa_length": 306,
"cds_start": 388,
"cds_end": null,
"cds_length": 921,
"cdna_start": 460,
"cdna_end": null,
"cdna_length": 1345,
"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": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC25A41",
"gene_hgnc_id": 28533,
"hgvs_c": "n.678T>C",
"hgvs_p": null,
"transcript": "ENST00000458275.6",
"protein_id": "ENSP00000405411.1",
"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": 1630,
"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": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC25A41",
"gene_hgnc_id": 28533,
"hgvs_c": "n.650T>C",
"hgvs_p": null,
"transcript": "NR_135612.2",
"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": 1389,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SLC25A41",
"gene_hgnc_id": 28533,
"dbsnp": "rs751725700",
"frequency_reference_population": 0.000006213079,
"hom_count_reference_population": 0,
"allele_count_reference_population": 10,
"gnomad_exomes_af": 0.00000617497,
"gnomad_genomes_af": 0.00000657851,
"gnomad_exomes_ac": 9,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9629395008087158,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.775,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.8737,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.28,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.267,
"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": 4,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PP3_Strong",
"acmg_by_gene": [
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PP3_Strong"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000321510.7",
"gene_symbol": "SLC25A41",
"hgnc_id": 28533,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.580T>C",
"hgvs_p": "p.Ser194Pro"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}