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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: 1-32895373-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=32895373&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 32895373,
"ref": "G",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000373463.8",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM54",
"gene_hgnc_id": 24143,
"hgvs_c": "c.526C>A",
"hgvs_p": "p.Arg176Ser",
"transcript": "NM_033504.4",
"protein_id": "NP_277039.1",
"transcript_support_level": null,
"aa_start": 176,
"aa_end": null,
"aa_length": 222,
"cds_start": 526,
"cds_end": null,
"cds_length": 669,
"cdna_start": 677,
"cdna_end": null,
"cdna_length": 1030,
"mane_select": "ENST00000373463.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM54",
"gene_hgnc_id": 24143,
"hgvs_c": "c.526C>A",
"hgvs_p": "p.Arg176Ser",
"transcript": "ENST00000373463.8",
"protein_id": "ENSP00000362562.3",
"transcript_support_level": 1,
"aa_start": 176,
"aa_end": null,
"aa_length": 222,
"cds_start": 526,
"cds_end": null,
"cds_length": 669,
"cdna_start": 677,
"cdna_end": null,
"cdna_length": 1030,
"mane_select": "NM_033504.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "S",
"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": "TMEM54",
"gene_hgnc_id": 24143,
"hgvs_c": "c.367C>A",
"hgvs_p": "p.Arg123Ser",
"transcript": "ENST00000329151.5",
"protein_id": "ENSP00000328630.5",
"transcript_support_level": 1,
"aa_start": 123,
"aa_end": null,
"aa_length": 169,
"cds_start": 367,
"cds_end": null,
"cds_length": 510,
"cdna_start": 518,
"cdna_end": null,
"cdna_length": 871,
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM54",
"gene_hgnc_id": 24143,
"hgvs_c": "n.666C>A",
"hgvs_p": null,
"transcript": "ENST00000475208.5",
"protein_id": null,
"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": 768,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM54",
"gene_hgnc_id": 24143,
"hgvs_c": "c.526C>A",
"hgvs_p": "p.Arg176Ser",
"transcript": "NM_001329722.2",
"protein_id": "NP_001316651.1",
"transcript_support_level": null,
"aa_start": 176,
"aa_end": null,
"aa_length": 240,
"cds_start": 526,
"cds_end": null,
"cds_length": 723,
"cdna_start": 677,
"cdna_end": null,
"cdna_length": 1084,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "S",
"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": "TMEM54",
"gene_hgnc_id": 24143,
"hgvs_c": "c.466C>A",
"hgvs_p": "p.Arg156Ser",
"transcript": "NM_001329723.2",
"protein_id": "NP_001316652.1",
"transcript_support_level": null,
"aa_start": 156,
"aa_end": null,
"aa_length": 202,
"cds_start": 466,
"cds_end": null,
"cds_length": 609,
"cdna_start": 617,
"cdna_end": null,
"cdna_length": 970,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM54",
"gene_hgnc_id": 24143,
"hgvs_c": "c.427C>A",
"hgvs_p": "p.Arg143Ser",
"transcript": "NM_001329724.2",
"protein_id": "NP_001316653.1",
"transcript_support_level": null,
"aa_start": 143,
"aa_end": null,
"aa_length": 189,
"cds_start": 427,
"cds_end": null,
"cds_length": 570,
"cdna_start": 578,
"cdna_end": null,
"cdna_length": 931,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "S",
"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": "TMEM54",
"gene_hgnc_id": 24143,
"hgvs_c": "c.367C>A",
"hgvs_p": "p.Arg123Ser",
"transcript": "NM_001329725.2",
"protein_id": "NP_001316654.1",
"transcript_support_level": null,
"aa_start": 123,
"aa_end": null,
"aa_length": 169,
"cds_start": 367,
"cds_end": null,
"cds_length": 510,
"cdna_start": 518,
"cdna_end": null,
"cdna_length": 871,
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM54",
"gene_hgnc_id": 24143,
"hgvs_c": "n.538C>A",
"hgvs_p": null,
"transcript": "ENST00000463914.1",
"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": 606,
"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": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM54",
"gene_hgnc_id": 24143,
"hgvs_c": "n.541C>A",
"hgvs_p": null,
"transcript": "ENST00000474144.5",
"protein_id": null,
"transcript_support_level": 3,
"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": 748,
"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": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM54",
"gene_hgnc_id": 24143,
"hgvs_c": "n.215C>A",
"hgvs_p": null,
"transcript": "ENST00000482771.1",
"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": 569,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "HPCA",
"gene_hgnc_id": 5144,
"hgvs_c": "n.106+1744G>T",
"hgvs_p": null,
"transcript": "ENST00000470896.1",
"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": 503,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "TMEM54",
"gene_hgnc_id": 24143,
"dbsnp": null,
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8963803648948669,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.371,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.5955,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.05,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 0.666,
"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": 4,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3_Moderate",
"acmg_by_gene": [
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000373463.8",
"gene_symbol": "TMEM54",
"hgnc_id": 24143,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.526C>A",
"hgvs_p": "p.Arg176Ser"
},
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000470896.1",
"gene_symbol": "HPCA",
"hgnc_id": 5144,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "n.106+1744G>T",
"hgvs_p": null
}
],
"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
}