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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: 14-36520101-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=14&pos=36520101&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 20,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "NKX2-1",
"hgnc_id": 11825,
"hgvs_c": "c.29G>A",
"hgvs_p": "p.Arg10Gln",
"inheritance_mode": "AD",
"pathogenic_score": 0,
"score": -20,
"transcript": "NM_001079668.3",
"verdict": "Benign"
},
{
"benign_score": 16,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS2"
],
"effects": [
"intron_variant"
],
"gene_symbol": "SFTA3",
"hgnc_id": null,
"hgvs_c": "n.-14+456G>A",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 0,
"score": -16,
"transcript": "ENST00000546983.2",
"verdict": "Benign"
},
{
"benign_score": 16,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS2"
],
"effects": [
"intron_variant"
],
"gene_symbol": "NKX2-1-AS1",
"hgnc_id": 40585,
"hgvs_c": "n.402+422C>T",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 0,
"score": -16,
"transcript": "ENST00000521292.2",
"verdict": "Benign"
},
{
"benign_score": 16,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS2"
],
"effects": [
"intron_variant"
],
"gene_symbol": "ENSG00000283098",
"hgnc_id": null,
"hgvs_c": "n.322+71264C>T",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 0,
"score": -16,
"transcript": "ENST00000634305.1",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BS1,BS2",
"acmg_score": -20,
"allele_count_reference_population": 854,
"alphamissense_prediction": null,
"alphamissense_score": 0.2272,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.32,
"chr": "14",
"clinvar_classification": "Benign/Likely benign",
"clinvar_disease": "Benign hereditary chorea,Brain-lung-thyroid syndrome,NKX2-1-related disorder,not provided",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:2 B:3",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.0073122382164001465,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 401,
"aa_ref": "R",
"aa_start": 10,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2190,
"cdna_start": 132,
"cds_end": null,
"cds_length": 1206,
"cds_start": 29,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "NM_001079668.3",
"gene_hgnc_id": 11825,
"gene_symbol": "NKX2-1",
"hgvs_c": "c.29G>A",
"hgvs_p": "p.Arg10Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000354822.7",
"protein_coding": true,
"protein_id": "NP_001073136.1",
"strand": false,
"transcript": "NM_001079668.3",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 401,
"aa_ref": "R",
"aa_start": 10,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2190,
"cdna_start": 132,
"cds_end": null,
"cds_length": 1206,
"cds_start": 29,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000354822.7",
"gene_hgnc_id": 11825,
"gene_symbol": "NKX2-1",
"hgvs_c": "c.29G>A",
"hgvs_p": "p.Arg10Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001079668.3",
"protein_coding": true,
"protein_id": "ENSP00000346879.6",
"strand": false,
"transcript": "ENST00000354822.7",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 371,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1962,
"cdna_start": null,
"cds_end": null,
"cds_length": 1116,
"cds_start": null,
"consequences": [
"5_prime_UTR_variant"
],
"exon_count": 5,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000522719.4",
"gene_hgnc_id": 11825,
"gene_symbol": "NKX2-1",
"hgvs_c": "c.-207G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000429519.4",
"strand": false,
"transcript": "ENST00000522719.4",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": true,
"cdna_end": null,
"cdna_length": 1664,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000546983.2",
"gene_hgnc_id": null,
"gene_symbol": "SFTA3",
"hgvs_c": "n.-14+456G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000449302.2",
"strand": false,
"transcript": "ENST00000546983.2",
"transcript_support_level": 4
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 371,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2583,
"cdna_start": null,
"cds_end": null,
"cds_length": 1116,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000518149.5",
"gene_hgnc_id": 11825,
"gene_symbol": "NKX2-1",
"hgvs_c": "c.-14+456G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000428341.1",
"strand": false,
"transcript": "ENST00000518149.5",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 1775,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000521292.2",
"gene_hgnc_id": 40585,
"gene_symbol": "NKX2-1-AS1",
"hgvs_c": "n.402+422C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000521292.2",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 1737,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000634305.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000283098",
"hgvs_c": "n.322+71264C>T",
"hgvs_p": null,
"intron_rank": 3,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000634305.1",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 822,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000716760.1",
"gene_hgnc_id": 40585,
"gene_symbol": "NKX2-1-AS1",
"hgvs_c": "n.88+422C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000716760.1",
"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": 1068,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000716761.1",
"gene_hgnc_id": 40585,
"gene_symbol": "NKX2-1-AS1",
"hgvs_c": "n.88+422C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000716761.1",
"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": 1775,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NR_103710.1",
"gene_hgnc_id": 40585,
"gene_symbol": "NKX2-1-AS1",
"hgvs_c": "n.402+422C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "NR_103710.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs201979429",
"effect": "missense_variant",
"frequency_reference_population": 0.00052939245,
"gene_hgnc_id": 11825,
"gene_symbol": "NKX2-1",
"gnomad_exomes_ac": 774,
"gnomad_exomes_af": 0.000529817,
"gnomad_exomes_homalt": 3,
"gnomad_genomes_ac": 80,
"gnomad_genomes_af": 0.00052532,
"gnomad_genomes_homalt": 1,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 4,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Benign/Likely benign",
"phenotype_combined": "Benign hereditary chorea|Brain-lung-thyroid syndrome|not provided|NKX2-1-related disorder",
"phylop100way_prediction": "Benign",
"phylop100way_score": 0.036,
"pos": 36520101,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.183,
"splice_prediction_selected": null,
"splice_score_selected": null,
"splice_source_selected": null,
"spliceai_max_prediction": null,
"spliceai_max_score": null,
"transcript": "NM_001079668.3"
}
]
}