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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: 1-1309210-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=1309210&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 1309210,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_001346116.2",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "L",
"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": "PUSL1",
"gene_hgnc_id": 26914,
"hgvs_c": "c.260C>T",
"hgvs_p": "p.Pro87Leu",
"transcript": "NM_153339.3",
"protein_id": "NP_699170.1",
"transcript_support_level": null,
"aa_start": 87,
"aa_end": null,
"aa_length": 303,
"cds_start": 260,
"cds_end": null,
"cds_length": 912,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000379031.10",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_153339.3"
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": true,
"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": "PUSL1",
"gene_hgnc_id": 26914,
"hgvs_c": "c.260C>T",
"hgvs_p": "p.Pro87Leu",
"transcript": "ENST00000379031.10",
"protein_id": "ENSP00000368318.5",
"transcript_support_level": 1,
"aa_start": 87,
"aa_end": null,
"aa_length": 303,
"cds_start": 260,
"cds_end": null,
"cds_length": 912,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_153339.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000379031.10"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_premature_start_codon_gain_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PUSL1",
"gene_hgnc_id": 26914,
"hgvs_c": "c.-224C>T",
"hgvs_p": null,
"transcript": "ENST00000467712.1",
"protein_id": "ENSP00000462968.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 124,
"cds_start": null,
"cds_end": null,
"cds_length": 377,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000467712.1"
},
{
"aa_ref": "P",
"aa_alt": "L",
"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": "PUSL1",
"gene_hgnc_id": 26914,
"hgvs_c": "c.260C>T",
"hgvs_p": "p.Pro87Leu",
"transcript": "NM_001346116.2",
"protein_id": "NP_001333045.1",
"transcript_support_level": null,
"aa_start": 87,
"aa_end": null,
"aa_length": 326,
"cds_start": 260,
"cds_end": null,
"cds_length": 981,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001346116.2"
},
{
"aa_ref": "P",
"aa_alt": "L",
"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": "PUSL1",
"gene_hgnc_id": 26914,
"hgvs_c": "c.260C>T",
"hgvs_p": "p.Pro87Leu",
"transcript": "ENST00000892133.1",
"protein_id": "ENSP00000562192.1",
"transcript_support_level": null,
"aa_start": 87,
"aa_end": null,
"aa_length": 326,
"cds_start": 260,
"cds_end": null,
"cds_length": 981,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000892133.1"
},
{
"aa_ref": "P",
"aa_alt": "L",
"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": "PUSL1",
"gene_hgnc_id": 26914,
"hgvs_c": "c.239C>T",
"hgvs_p": "p.Pro80Leu",
"transcript": "ENST00000892132.1",
"protein_id": "ENSP00000562191.1",
"transcript_support_level": null,
"aa_start": 80,
"aa_end": null,
"aa_length": 296,
"cds_start": 239,
"cds_end": null,
"cds_length": 891,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000892132.1"
},
{
"aa_ref": "P",
"aa_alt": "L",
"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": "PUSL1",
"gene_hgnc_id": 26914,
"hgvs_c": "c.260C>T",
"hgvs_p": "p.Pro87Leu",
"transcript": "XM_024453057.2",
"protein_id": "XP_024308825.1",
"transcript_support_level": null,
"aa_start": 87,
"aa_end": null,
"aa_length": 394,
"cds_start": 260,
"cds_end": null,
"cds_length": 1185,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_024453057.2"
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PUSL1",
"gene_hgnc_id": 26914,
"hgvs_c": "c.260C>T",
"hgvs_p": "p.Pro87Leu",
"transcript": "XM_047444716.1",
"protein_id": "XP_047300672.1",
"transcript_support_level": null,
"aa_start": 87,
"aa_end": null,
"aa_length": 242,
"cds_start": 260,
"cds_end": null,
"cds_length": 729,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047444716.1"
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PUSL1",
"gene_hgnc_id": 26914,
"hgvs_c": "c.260C>T",
"hgvs_p": "p.Pro87Leu",
"transcript": "XM_005244720.5",
"protein_id": "XP_005244777.1",
"transcript_support_level": null,
"aa_start": 87,
"aa_end": null,
"aa_length": 228,
"cds_start": 260,
"cds_end": null,
"cds_length": 687,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005244720.5"
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PUSL1",
"gene_hgnc_id": 26914,
"hgvs_c": "c.260C>T",
"hgvs_p": "p.Pro87Leu",
"transcript": "XM_047444722.1",
"protein_id": "XP_047300678.1",
"transcript_support_level": null,
"aa_start": 87,
"aa_end": null,
"aa_length": 228,
"cds_start": 260,
"cds_end": null,
"cds_length": 687,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047444722.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PUSL1",
"gene_hgnc_id": 26914,
"hgvs_c": "c.-224C>T",
"hgvs_p": null,
"transcript": "ENST00000467712.1",
"protein_id": "ENSP00000462968.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 124,
"cds_start": null,
"cds_end": null,
"cds_length": 377,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000467712.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PUSL1",
"gene_hgnc_id": 26914,
"hgvs_c": "n.310C>T",
"hgvs_p": null,
"transcript": "ENST00000463758.1",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000463758.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PUSL1",
"gene_hgnc_id": 26914,
"hgvs_c": "n.235C>T",
"hgvs_p": null,
"transcript": "ENST00000470520.5",
"protein_id": null,
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000470520.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PUSL1",
"gene_hgnc_id": 26914,
"hgvs_c": "n.39C>T",
"hgvs_p": null,
"transcript": "ENST00000706601.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000706601.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PUSL1",
"gene_hgnc_id": 26914,
"hgvs_c": "n.249C>T",
"hgvs_p": null,
"transcript": "NR_144369.2",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_144369.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ACAP3",
"gene_hgnc_id": 16754,
"hgvs_c": "n.168+232G>A",
"hgvs_p": null,
"transcript": "ENST00000472541.5",
"protein_id": null,
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000472541.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PUSL1",
"gene_hgnc_id": 26914,
"hgvs_c": "n.-25C>T",
"hgvs_p": null,
"transcript": "ENST00000493657.1",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000493657.1"
}
],
"gene_symbol": "PUSL1",
"gene_hgnc_id": 26914,
"dbsnp": "rs1045224696",
"frequency_reference_population": 0.00002101417,
"hom_count_reference_population": 0,
"allele_count_reference_population": 32,
"gnomad_exomes_af": 0.0000226185,
"gnomad_genomes_af": 0.00000656927,
"gnomad_exomes_ac": 31,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.1488475203514099,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.042,
"revel_prediction": "Benign",
"alphamissense_score": 0.1029,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.52,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.438,
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_001346116.2",
"gene_symbol": "PUSL1",
"hgnc_id": 26914,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.260C>T",
"hgvs_p": "p.Pro87Leu"
},
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000472541.5",
"gene_symbol": "ACAP3",
"hgnc_id": 16754,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "n.168+232G>A",
"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
}