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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: 1-214364515-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=214364515&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 5,
"criteria": [
"BP4_Moderate",
"BP6_Moderate",
"BP7"
],
"effects": [
"synonymous_variant"
],
"gene_symbol": "PTPN14",
"hgnc_id": 9647,
"hgvs_c": "c.3432C>T",
"hgvs_p": "p.Asn1144Asn",
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -5,
"transcript": "NM_005401.5",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate,BP6_Moderate,BP7",
"acmg_score": -5,
"allele_count_reference_population": 107,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.39,
"chr": "1",
"clinvar_classification": "Likely benign",
"clinvar_disease": "not provided",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.38999998569488525,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 1187,
"aa_ref": "N",
"aa_start": 1144,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 13360,
"cdna_start": 4006,
"cds_end": null,
"cds_length": 3564,
"cds_start": 3432,
"consequences": [
"synonymous_variant"
],
"exon_count": 19,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "NM_005401.5",
"gene_hgnc_id": 9647,
"gene_symbol": "PTPN14",
"hgvs_c": "c.3432C>T",
"hgvs_p": "p.Asn1144Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000366956.10",
"protein_coding": true,
"protein_id": "NP_005392.2",
"strand": false,
"transcript": "NM_005401.5",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 1187,
"aa_ref": "N",
"aa_start": 1144,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 13360,
"cdna_start": 4006,
"cds_end": null,
"cds_length": 3564,
"cds_start": 3432,
"consequences": [
"synonymous_variant"
],
"exon_count": 19,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "ENST00000366956.10",
"gene_hgnc_id": 9647,
"gene_symbol": "PTPN14",
"hgvs_c": "c.3432C>T",
"hgvs_p": "p.Asn1144Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_005401.5",
"protein_coding": true,
"protein_id": "ENSP00000355923.4",
"strand": false,
"transcript": "ENST00000366956.10",
"transcript_support_level": 1
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 1187,
"aa_ref": "N",
"aa_start": 1144,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 13451,
"cdna_start": 4097,
"cds_end": null,
"cds_length": 3564,
"cds_start": 3432,
"consequences": [
"synonymous_variant"
],
"exon_count": 20,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "XM_017001941.2",
"gene_hgnc_id": 9647,
"gene_symbol": "PTPN14",
"hgvs_c": "c.3432C>T",
"hgvs_p": "p.Asn1144Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016857430.1",
"strand": false,
"transcript": "XM_017001941.2",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 1187,
"aa_ref": "N",
"aa_start": 1144,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 13514,
"cdna_start": 4160,
"cds_end": null,
"cds_length": 3564,
"cds_start": 3432,
"consequences": [
"synonymous_variant"
],
"exon_count": 21,
"exon_rank": 20,
"exon_rank_end": null,
"feature": "XM_024448759.2",
"gene_hgnc_id": 9647,
"gene_symbol": "PTPN14",
"hgvs_c": "c.3432C>T",
"hgvs_p": "p.Asn1144Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_024304527.1",
"strand": false,
"transcript": "XM_024448759.2",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 1187,
"aa_ref": "N",
"aa_start": 1144,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 14304,
"cdna_start": 4950,
"cds_end": null,
"cds_length": 3564,
"cds_start": 3432,
"consequences": [
"synonymous_variant"
],
"exon_count": 20,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "XM_047426367.1",
"gene_hgnc_id": 9647,
"gene_symbol": "PTPN14",
"hgvs_c": "c.3432C>T",
"hgvs_p": "p.Asn1144Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047282323.1",
"strand": false,
"transcript": "XM_047426367.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 1187,
"aa_ref": "N",
"aa_start": 1144,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 13591,
"cdna_start": 4237,
"cds_end": null,
"cds_length": 3564,
"cds_start": 3432,
"consequences": [
"synonymous_variant"
],
"exon_count": 19,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "XM_047426370.1",
"gene_hgnc_id": 9647,
"gene_symbol": "PTPN14",
"hgvs_c": "c.3432C>T",
"hgvs_p": "p.Asn1144Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047282326.1",
"strand": false,
"transcript": "XM_047426370.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 1187,
"aa_ref": "N",
"aa_start": 1144,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 13356,
"cdna_start": 4002,
"cds_end": null,
"cds_length": 3564,
"cds_start": 3432,
"consequences": [
"synonymous_variant"
],
"exon_count": 19,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "XM_047426374.1",
"gene_hgnc_id": 9647,
"gene_symbol": "PTPN14",
"hgvs_c": "c.3432C>T",
"hgvs_p": "p.Asn1144Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047282330.1",
"strand": false,
"transcript": "XM_047426374.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 211,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3842,
"cdna_start": null,
"cds_end": null,
"cds_length": 636,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 18,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "ENST00000543945.5",
"gene_hgnc_id": 9647,
"gene_symbol": "PTPN14",
"hgvs_c": "c.*2708C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000443330.1",
"strand": false,
"transcript": "ENST00000543945.5",
"transcript_support_level": 5
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs374113328",
"effect": "synonymous_variant",
"frequency_reference_population": 0.000066312256,
"gene_hgnc_id": 9647,
"gene_symbol": "PTPN14",
"gnomad_exomes_ac": 92,
"gnomad_exomes_af": 0.0000629453,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 15,
"gnomad_genomes_af": 0.0000986894,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Likely benign",
"phenotype_combined": "not provided",
"phylop100way_prediction": "Benign",
"phylop100way_score": 0.512,
"pos": 214364515,
"ref": "G",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_005401.5"
}
]
}