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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: 12-114385563-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=114385563&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PS3",
"PM2",
"PP3_Strong",
"PP5_Very_Strong"
],
"effects": [
"missense_variant"
],
"gene_symbol": "TBX5",
"hgnc_id": 11604,
"hgvs_c": "c.668C>T",
"hgvs_p": "p.Thr223Met",
"inheritance_mode": "AD",
"pathogenic_score": 18,
"score": 18,
"transcript": "NM_000192.3",
"verdict": "Pathogenic"
}
],
"acmg_classification": "Pathogenic",
"acmg_criteria": "PS3,PM2,PP3_Strong,PP5_Very_Strong",
"acmg_score": 18,
"allele_count_reference_population": 0,
"alphamissense_prediction": null,
"alphamissense_score": 0.9999,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.45,
"chr": "12",
"clinvar_classification": "Pathogenic",
"clinvar_disease": "Aortic valve disease 2,Holt-Oram syndrome,not provided",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:3",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.9498755931854248,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 518,
"aa_ref": "T",
"aa_start": 223,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3733,
"cdna_start": 1223,
"cds_end": null,
"cds_length": 1557,
"cds_start": 668,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "NM_181486.4",
"gene_hgnc_id": 11604,
"gene_symbol": "TBX5",
"hgvs_c": "c.668C>T",
"hgvs_p": "p.Thr223Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000405440.7",
"protein_coding": true,
"protein_id": "NP_852259.1",
"strand": false,
"transcript": "NM_181486.4",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 518,
"aa_ref": "T",
"aa_start": 223,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 3733,
"cdna_start": 1223,
"cds_end": null,
"cds_length": 1557,
"cds_start": 668,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000405440.7",
"gene_hgnc_id": 11604,
"gene_symbol": "TBX5",
"hgvs_c": "c.668C>T",
"hgvs_p": "p.Thr223Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_181486.4",
"protein_coding": true,
"protein_id": "ENSP00000384152.3",
"strand": false,
"transcript": "ENST00000405440.7",
"transcript_support_level": 1
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 518,
"aa_ref": "T",
"aa_start": 223,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3825,
"cdna_start": 1335,
"cds_end": null,
"cds_length": 1557,
"cds_start": 668,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000310346.8",
"gene_hgnc_id": 11604,
"gene_symbol": "TBX5",
"hgvs_c": "c.668C>T",
"hgvs_p": "p.Thr223Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000309913.4",
"strand": false,
"transcript": "ENST00000310346.8",
"transcript_support_level": 1
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 468,
"aa_ref": "T",
"aa_start": 173,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3585,
"cdna_start": 1095,
"cds_end": null,
"cds_length": 1407,
"cds_start": 518,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000349716.9",
"gene_hgnc_id": 11604,
"gene_symbol": "TBX5",
"hgvs_c": "c.518C>T",
"hgvs_p": "p.Thr173Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000337723.5",
"strand": false,
"transcript": "ENST00000349716.9",
"transcript_support_level": 1
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 349,
"aa_ref": "T",
"aa_start": 223,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1050,
"cdna_start": 668,
"cds_end": null,
"cds_length": 1050,
"cds_start": 668,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000526441.1",
"gene_hgnc_id": 11604,
"gene_symbol": "TBX5",
"hgvs_c": "c.668C>T",
"hgvs_p": "p.Thr223Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000433292.1",
"strand": false,
"transcript": "ENST00000526441.1",
"transcript_support_level": 1
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 518,
"aa_ref": "T",
"aa_start": 223,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3826,
"cdna_start": 1335,
"cds_end": null,
"cds_length": 1557,
"cds_start": 668,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "NM_000192.3",
"gene_hgnc_id": 11604,
"gene_symbol": "TBX5",
"hgvs_c": "c.668C>T",
"hgvs_p": "p.Thr223Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_000183.2",
"strand": false,
"transcript": "NM_000192.3",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 518,
"aa_ref": "T",
"aa_start": 223,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3058,
"cdna_start": 1931,
"cds_end": null,
"cds_length": 1557,
"cds_start": 668,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000860921.1",
"gene_hgnc_id": 11604,
"gene_symbol": "TBX5",
"hgvs_c": "c.668C>T",
"hgvs_p": "p.Thr223Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000530980.1",
"strand": false,
"transcript": "ENST00000860921.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 518,
"aa_ref": "T",
"aa_start": 223,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3410,
"cdna_start": 919,
"cds_end": null,
"cds_length": 1557,
"cds_start": 668,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000860922.1",
"gene_hgnc_id": 11604,
"gene_symbol": "TBX5",
"hgvs_c": "c.668C>T",
"hgvs_p": "p.Thr223Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000530981.1",
"strand": false,
"transcript": "ENST00000860922.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 518,
"aa_ref": "T",
"aa_start": 223,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3719,
"cdna_start": 1228,
"cds_end": null,
"cds_length": 1557,
"cds_start": 668,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000860923.1",
"gene_hgnc_id": 11604,
"gene_symbol": "TBX5",
"hgvs_c": "c.668C>T",
"hgvs_p": "p.Thr223Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000530982.1",
"strand": false,
"transcript": "ENST00000860923.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 518,
"aa_ref": "T",
"aa_start": 223,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3766,
"cdna_start": 1257,
"cds_end": null,
"cds_length": 1557,
"cds_start": 668,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000860924.1",
"gene_hgnc_id": 11604,
"gene_symbol": "TBX5",
"hgvs_c": "c.668C>T",
"hgvs_p": "p.Thr223Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000530983.1",
"strand": false,
"transcript": "ENST00000860924.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 518,
"aa_ref": "T",
"aa_start": 223,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3472,
"cdna_start": 978,
"cds_end": null,
"cds_length": 1557,
"cds_start": 668,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000860925.1",
"gene_hgnc_id": 11604,
"gene_symbol": "TBX5",
"hgvs_c": "c.668C>T",
"hgvs_p": "p.Thr223Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000530984.1",
"strand": false,
"transcript": "ENST00000860925.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 518,
"aa_ref": "T",
"aa_start": 223,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3326,
"cdna_start": 1010,
"cds_end": null,
"cds_length": 1557,
"cds_start": 668,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000860926.1",
"gene_hgnc_id": 11604,
"gene_symbol": "TBX5",
"hgvs_c": "c.668C>T",
"hgvs_p": "p.Thr223Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000530985.1",
"strand": false,
"transcript": "ENST00000860926.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 518,
"aa_ref": "T",
"aa_start": 223,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2110,
"cdna_start": 779,
"cds_end": null,
"cds_length": 1557,
"cds_start": 668,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000860927.1",
"gene_hgnc_id": 11604,
"gene_symbol": "TBX5",
"hgvs_c": "c.668C>T",
"hgvs_p": "p.Thr223Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000530986.1",
"strand": false,
"transcript": "ENST00000860927.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 518,
"aa_ref": "T",
"aa_start": 223,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2533,
"cdna_start": 1208,
"cds_end": null,
"cds_length": 1557,
"cds_start": 668,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000860928.1",
"gene_hgnc_id": 11604,
"gene_symbol": "TBX5",
"hgvs_c": "c.668C>T",
"hgvs_p": "p.Thr223Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000530987.1",
"strand": false,
"transcript": "ENST00000860928.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 518,
"aa_ref": "T",
"aa_start": 223,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3393,
"cdna_start": 884,
"cds_end": null,
"cds_length": 1557,
"cds_start": 668,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000945349.1",
"gene_hgnc_id": 11604,
"gene_symbol": "TBX5",
"hgvs_c": "c.668C>T",
"hgvs_p": "p.Thr223Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000615408.1",
"strand": false,
"transcript": "ENST00000945349.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 518,
"aa_ref": "T",
"aa_start": 223,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3498,
"cdna_start": 1009,
"cds_end": null,
"cds_length": 1557,
"cds_start": 668,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000945350.1",
"gene_hgnc_id": 11604,
"gene_symbol": "TBX5",
"hgvs_c": "c.668C>T",
"hgvs_p": "p.Thr223Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000615409.1",
"strand": false,
"transcript": "ENST00000945350.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 518,
"aa_ref": "T",
"aa_start": 223,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2592,
"cdna_start": 1259,
"cds_end": null,
"cds_length": 1557,
"cds_start": 668,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000945351.1",
"gene_hgnc_id": 11604,
"gene_symbol": "TBX5",
"hgvs_c": "c.668C>T",
"hgvs_p": "p.Thr223Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000615410.1",
"strand": false,
"transcript": "ENST00000945351.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 468,
"aa_ref": "T",
"aa_start": 173,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3230,
"cdna_start": 720,
"cds_end": null,
"cds_length": 1407,
"cds_start": 518,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "NM_080717.4",
"gene_hgnc_id": 11604,
"gene_symbol": "TBX5",
"hgvs_c": "c.518C>T",
"hgvs_p": "p.Thr173Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_542448.1",
"strand": false,
"transcript": "NM_080717.4",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 534,
"aa_ref": "T",
"aa_start": 239,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4900,
"cdna_start": 2390,
"cds_end": null,
"cds_length": 1605,
"cds_start": 716,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "XM_017019912.2",
"gene_hgnc_id": 11604,
"gene_symbol": "TBX5",
"hgvs_c": "c.716C>T",
"hgvs_p": "p.Thr239Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016875401.1",
"strand": false,
"transcript": "XM_017019912.2",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs1555225344",
"effect": "missense_variant",
"frequency_reference_population": null,
"gene_hgnc_id": 11604,
"gene_symbol": "TBX5",
"gnomad_exomes_ac": null,
"gnomad_exomes_af": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Pathogenic",
"phenotype_combined": "not provided|Aortic valve disease 2|Holt-Oram syndrome",
"phylop100way_prediction": "Pathogenic",
"phylop100way_score": 9.488,
"pos": 114385563,
"ref": "G",
"revel_prediction": "Pathogenic",
"revel_score": 0.959,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_000192.3"
}
]
}