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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: 1-155295457-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=155295457&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 155295457,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000342741.6",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKLR",
"gene_hgnc_id": 9020,
"hgvs_c": "c.487C>T",
"hgvs_p": "p.Arg163Cys",
"transcript": "NM_000298.6",
"protein_id": "NP_000289.1",
"transcript_support_level": null,
"aa_start": 163,
"aa_end": null,
"aa_length": 574,
"cds_start": 487,
"cds_end": null,
"cds_length": 1725,
"cdna_start": 530,
"cdna_end": null,
"cdna_length": 3047,
"mane_select": "ENST00000342741.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKLR",
"gene_hgnc_id": 9020,
"hgvs_c": "c.487C>T",
"hgvs_p": "p.Arg163Cys",
"transcript": "ENST00000342741.6",
"protein_id": "ENSP00000339933.4",
"transcript_support_level": 1,
"aa_start": 163,
"aa_end": null,
"aa_length": 574,
"cds_start": 487,
"cds_end": null,
"cds_length": 1725,
"cdna_start": 530,
"cdna_end": null,
"cdna_length": 3047,
"mane_select": "NM_000298.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKLR",
"gene_hgnc_id": 9020,
"hgvs_c": "c.394C>T",
"hgvs_p": "p.Arg132Cys",
"transcript": "ENST00000392414.7",
"protein_id": "ENSP00000376214.3",
"transcript_support_level": 1,
"aa_start": 132,
"aa_end": null,
"aa_length": 543,
"cds_start": 394,
"cds_end": null,
"cds_length": 1632,
"cdna_start": 508,
"cdna_end": null,
"cdna_length": 2479,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKLR",
"gene_hgnc_id": 9020,
"hgvs_c": "c.394C>T",
"hgvs_p": "p.Arg132Cys",
"transcript": "NM_181871.4",
"protein_id": "NP_870986.1",
"transcript_support_level": null,
"aa_start": 132,
"aa_end": null,
"aa_length": 543,
"cds_start": 394,
"cds_end": null,
"cds_length": 1632,
"cdna_start": 459,
"cdna_end": null,
"cdna_length": 2976,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKLR",
"gene_hgnc_id": 9020,
"hgvs_c": "c.295C>T",
"hgvs_p": "p.Arg99Cys",
"transcript": "ENST00000434082.3",
"protein_id": "ENSP00000398037.3",
"transcript_support_level": 5,
"aa_start": 99,
"aa_end": null,
"aa_length": 160,
"cds_start": 295,
"cds_end": null,
"cds_length": 483,
"cdna_start": 392,
"cdna_end": null,
"cdna_length": 580,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKLR",
"gene_hgnc_id": 9020,
"hgvs_c": "c.487C>T",
"hgvs_p": "p.Arg163Cys",
"transcript": "XM_047422591.1",
"protein_id": "XP_047278547.1",
"transcript_support_level": null,
"aa_start": 163,
"aa_end": null,
"aa_length": 574,
"cds_start": 487,
"cds_end": null,
"cds_length": 1725,
"cdna_start": 609,
"cdna_end": null,
"cdna_length": 3126,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKLR",
"gene_hgnc_id": 9020,
"hgvs_c": "c.487C>T",
"hgvs_p": "p.Arg163Cys",
"transcript": "XM_047422592.1",
"protein_id": "XP_047278548.1",
"transcript_support_level": null,
"aa_start": 163,
"aa_end": null,
"aa_length": 574,
"cds_start": 487,
"cds_end": null,
"cds_length": 1725,
"cdna_start": 720,
"cdna_end": null,
"cdna_length": 3237,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKLR",
"gene_hgnc_id": 9020,
"hgvs_c": "c.295C>T",
"hgvs_p": "p.Arg99Cys",
"transcript": "XM_006711386.5",
"protein_id": "XP_006711449.1",
"transcript_support_level": null,
"aa_start": 99,
"aa_end": null,
"aa_length": 510,
"cds_start": 295,
"cds_end": null,
"cds_length": 1533,
"cdna_start": 388,
"cdna_end": null,
"cdna_length": 2905,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKLR",
"gene_hgnc_id": 9020,
"hgvs_c": "c.295C>T",
"hgvs_p": "p.Arg99Cys",
"transcript": "XM_011509640.4",
"protein_id": "XP_011507942.1",
"transcript_support_level": null,
"aa_start": 99,
"aa_end": null,
"aa_length": 510,
"cds_start": 295,
"cds_end": null,
"cds_length": 1533,
"cdna_start": 440,
"cdna_end": null,
"cdna_length": 2957,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKLR",
"gene_hgnc_id": 9020,
"hgvs_c": "c.487C>T",
"hgvs_p": "p.Arg163Cys",
"transcript": "XM_017001493.1",
"protein_id": "XP_016856982.1",
"transcript_support_level": null,
"aa_start": 163,
"aa_end": null,
"aa_length": 383,
"cds_start": 487,
"cds_end": null,
"cds_length": 1152,
"cdna_start": 508,
"cdna_end": null,
"cdna_length": 1273,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PKLR",
"gene_hgnc_id": 9020,
"dbsnp": "rs118204083",
"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": 0.9917731285095215,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.917,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.8203,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.52,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 3.278,
"phylop100way_prediction": "Benign",
"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": 9,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM1,PM2,PP2,PP3_Strong",
"acmg_by_gene": [
{
"score": 9,
"benign_score": 0,
"pathogenic_score": 9,
"criteria": [
"PM1",
"PM2",
"PP2",
"PP3_Strong"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000342741.6",
"gene_symbol": "PKLR",
"hgnc_id": 9020,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.487C>T",
"hgvs_p": "p.Arg163Cys"
}
],
"clinvar_disease": "Pyruvate kinase deficiency of red cells,not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Pyruvate kinase deficiency of red cells|not provided",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}