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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: 12-98544517-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=98544517&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 98544517,
"ref": "G",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000556029.6",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMPO",
"gene_hgnc_id": 11875,
"hgvs_c": "c.859G>C",
"hgvs_p": "p.Ala287Pro",
"transcript": "NM_001032283.3",
"protein_id": "NP_001027454.1",
"transcript_support_level": null,
"aa_start": 287,
"aa_end": null,
"aa_length": 454,
"cds_start": 859,
"cds_end": null,
"cds_length": 1365,
"cdna_start": 1137,
"cdna_end": null,
"cdna_length": 4136,
"mane_select": "ENST00000556029.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "P",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMPO",
"gene_hgnc_id": 11875,
"hgvs_c": "c.859G>C",
"hgvs_p": "p.Ala287Pro",
"transcript": "ENST00000556029.6",
"protein_id": "ENSP00000450627.1",
"transcript_support_level": 1,
"aa_start": 287,
"aa_end": null,
"aa_length": 454,
"cds_start": 859,
"cds_end": null,
"cds_length": 1365,
"cdna_start": 1137,
"cdna_end": null,
"cdna_length": 4136,
"mane_select": "NM_001032283.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "TMPO",
"gene_hgnc_id": 11875,
"hgvs_c": "c.664-1842G>C",
"hgvs_p": null,
"transcript": "ENST00000393053.6",
"protein_id": "ENSP00000376773.2",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 345,
"cds_start": -4,
"cds_end": null,
"cds_length": 1038,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2374,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMPO",
"gene_hgnc_id": 11875,
"hgvs_c": "c.859G>C",
"hgvs_p": "p.Ala287Pro",
"transcript": "ENST00000715724.1",
"protein_id": "ENSP00000520506.1",
"transcript_support_level": null,
"aa_start": 287,
"aa_end": null,
"aa_length": 454,
"cds_start": 859,
"cds_end": null,
"cds_length": 1365,
"cdna_start": 1166,
"cdna_end": null,
"cdna_length": 4165,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMPO",
"gene_hgnc_id": 11875,
"hgvs_c": "c.739G>C",
"hgvs_p": "p.Ala247Pro",
"transcript": "NM_001307975.2",
"protein_id": "NP_001294904.1",
"transcript_support_level": null,
"aa_start": 247,
"aa_end": null,
"aa_length": 414,
"cds_start": 739,
"cds_end": null,
"cds_length": 1245,
"cdna_start": 1017,
"cdna_end": null,
"cdna_length": 4016,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMPO",
"gene_hgnc_id": 11875,
"hgvs_c": "c.739G>C",
"hgvs_p": "p.Ala247Pro",
"transcript": "ENST00000343315.9",
"protein_id": "ENSP00000340251.5",
"transcript_support_level": 5,
"aa_start": 247,
"aa_end": null,
"aa_length": 414,
"cds_start": 739,
"cds_end": null,
"cds_length": 1245,
"cdna_start": 989,
"cdna_end": null,
"cdna_length": 2465,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMPO",
"gene_hgnc_id": 11875,
"hgvs_c": "n.224G>C",
"hgvs_p": null,
"transcript": "ENST00000548223.5",
"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": 736,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "TMPO",
"gene_hgnc_id": 11875,
"hgvs_c": "c.664-1842G>C",
"hgvs_p": null,
"transcript": "NM_001032284.3",
"protein_id": "NP_001027455.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 345,
"cds_start": -4,
"cds_end": null,
"cds_length": 1038,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3809,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "TMPO",
"gene_hgnc_id": 11875,
"hgvs_c": "c.385-434G>C",
"hgvs_p": null,
"transcript": "ENST00000556678.1",
"protein_id": "ENSP00000451552.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 236,
"cds_start": -4,
"cds_end": null,
"cds_length": 713,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 713,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "TMPO",
"gene_hgnc_id": 11875,
"hgvs_c": "c.664-434G>C",
"hgvs_p": null,
"transcript": "XM_005269132.5",
"protein_id": "XP_005269189.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 382,
"cds_start": -4,
"cds_end": null,
"cds_length": 1149,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3937,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMPO",
"gene_hgnc_id": 11875,
"hgvs_c": "n.-122G>C",
"hgvs_p": null,
"transcript": "ENST00000551987.1",
"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": 727,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "TMPO",
"gene_hgnc_id": 11875,
"dbsnp": "rs7133258",
"frequency_reference_population": 0.010104504,
"hom_count_reference_population": 141,
"allele_count_reference_population": 16298,
"gnomad_exomes_af": 0.0102009,
"gnomad_genomes_af": 0.00917907,
"gnomad_exomes_ac": 14901,
"gnomad_genomes_ac": 1397,
"gnomad_exomes_homalt": 124,
"gnomad_genomes_homalt": 17,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.003778129816055298,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": null,
"splice_prediction_selected": null,
"splice_source_selected": null,
"revel_score": 0.067,
"revel_prediction": "Benign",
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.39,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.99,
"phylop100way_prediction": "Benign",
"spliceai_max_score": null,
"spliceai_max_prediction": null,
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -16,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BS2",
"acmg_by_gene": [
{
"score": -16,
"benign_score": 16,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000556029.6",
"gene_symbol": "TMPO",
"hgnc_id": 11875,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.859G>C",
"hgvs_p": "p.Ala287Pro"
}
],
"clinvar_disease": "TMPO-related disorder,not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:5",
"phenotype_combined": "not specified|not provided|TMPO-related disorder",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}