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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: 19-41342229-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=41342229&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PS3",
"PM1",
"PM2",
"PM5",
"PP3_Moderate",
"PP5_Very_Strong"
],
"effects": [
"missense_variant"
],
"gene_symbol": "TGFB1",
"hgnc_id": 11766,
"hgvs_c": "c.653G>A",
"hgvs_p": "p.Arg218His",
"inheritance_mode": "AD,AR",
"pathogenic_score": 20,
"score": 20,
"transcript": "NM_000660.7",
"verdict": "Pathogenic"
}
],
"acmg_classification": "Pathogenic",
"acmg_criteria": "PS3,PM1,PM2,PM5,PP3_Moderate,PP5_Very_Strong",
"acmg_score": 20,
"allele_count_reference_population": 4,
"alphamissense_prediction": "Benign",
"alphamissense_score": 0.2801,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Uncertain_significance",
"bayesdelnoaf_score": 0.12,
"chr": "19",
"clinvar_classification": "Pathogenic",
"clinvar_disease": "Diaphyseal dysplasia,Inborn genetic diseases,not provided",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:5 O:1",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.9103769063949585,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 390,
"aa_ref": "R",
"aa_start": 218,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2780,
"cdna_start": 1531,
"cds_end": null,
"cds_length": 1173,
"cds_start": 653,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "NM_000660.7",
"gene_hgnc_id": 11766,
"gene_symbol": "TGFB1",
"hgvs_c": "c.653G>A",
"hgvs_p": "p.Arg218His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000221930.6",
"protein_coding": true,
"protein_id": "NP_000651.3",
"strand": false,
"transcript": "NM_000660.7",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 390,
"aa_ref": "R",
"aa_start": 218,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2780,
"cdna_start": 1531,
"cds_end": null,
"cds_length": 1173,
"cds_start": 653,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000221930.6",
"gene_hgnc_id": 11766,
"gene_symbol": "TGFB1",
"hgvs_c": "c.653G>A",
"hgvs_p": "p.Arg218His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_000660.7",
"protein_coding": true,
"protein_id": "ENSP00000221930.4",
"strand": false,
"transcript": "ENST00000221930.6",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 392,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000597453.1",
"gene_hgnc_id": 11766,
"gene_symbol": "TGFB1",
"hgvs_c": "n.184G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000597453.1",
"transcript_support_level": 1
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 391,
"aa_ref": "R",
"aa_start": 218,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3416,
"cdna_start": 1570,
"cds_end": null,
"cds_length": 1176,
"cds_start": 653,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000890114.1",
"gene_hgnc_id": 11766,
"gene_symbol": "TGFB1",
"hgvs_c": "c.653G>A",
"hgvs_p": "p.Arg218His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000560173.1",
"strand": false,
"transcript": "ENST00000890114.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 370,
"aa_ref": "R",
"aa_start": 218,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1250,
"cdna_start": 653,
"cds_end": null,
"cds_length": 1113,
"cds_start": 653,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000600196.2",
"gene_hgnc_id": 11766,
"gene_symbol": "TGFB1",
"hgvs_c": "c.653G>A",
"hgvs_p": "p.Arg218His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000504008.1",
"strand": false,
"transcript": "ENST00000600196.2",
"transcript_support_level": 5
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 370,
"aa_ref": "R",
"aa_start": 198,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2134,
"cdna_start": 1471,
"cds_end": null,
"cds_length": 1113,
"cds_start": 593,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000966383.1",
"gene_hgnc_id": 11766,
"gene_symbol": "TGFB1",
"hgvs_c": "c.593G>A",
"hgvs_p": "p.Arg198His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000636442.1",
"strand": false,
"transcript": "ENST00000966383.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 298,
"aa_ref": "R",
"aa_start": 125,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1663,
"cdna_start": 1004,
"cds_end": null,
"cds_length": 897,
"cds_start": 374,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000966384.1",
"gene_hgnc_id": 11766,
"gene_symbol": "TGFB1",
"hgvs_c": "c.374G>A",
"hgvs_p": "p.Arg125His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000636443.1",
"strand": false,
"transcript": "ENST00000966384.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 391,
"aa_ref": "R",
"aa_start": 218,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2783,
"cdna_start": 1531,
"cds_end": null,
"cds_length": 1176,
"cds_start": 653,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "XM_011527242.3",
"gene_hgnc_id": 11766,
"gene_symbol": "TGFB1",
"hgvs_c": "c.653G>A",
"hgvs_p": "p.Arg218His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011525544.1",
"strand": false,
"transcript": "XM_011527242.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 306,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1084,
"cdna_start": null,
"cds_end": null,
"cds_length": 921,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000677934.1",
"gene_hgnc_id": 11766,
"gene_symbol": "TGFB1",
"hgvs_c": "c.634+2518G>A",
"hgvs_p": null,
"intron_rank": 3,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000504769.1",
"strand": false,
"transcript": "ENST00000677934.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 559,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000598758.5",
"gene_hgnc_id": 11766,
"gene_symbol": "TGFB1",
"hgvs_c": "n.-199G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000598758.5",
"transcript_support_level": 5
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs104894720",
"effect": "missense_variant",
"frequency_reference_population": 0.0000027591268,
"gene_hgnc_id": 11766,
"gene_symbol": "TGFB1",
"gnomad_exomes_ac": 4,
"gnomad_exomes_af": 0.00000275913,
"gnomad_exomes_homalt": 0,
"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": "Diaphyseal dysplasia|not provided|Inborn genetic diseases",
"phylop100way_prediction": "Benign",
"phylop100way_score": 2.451,
"pos": 41342229,
"ref": "C",
"revel_prediction": "Uncertain_significance",
"revel_score": 0.407,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.019999999552965164,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.02,
"transcript": "NM_000660.7"
}
]
}