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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: 2-218395009-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=218395009&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 12,
"criteria": [
"BP4_Strong",
"BA1"
],
"effects": [
"missense_variant"
],
"gene_symbol": "SLC11A1",
"hgnc_id": 10907,
"hgvs_c": "c.1627G>A",
"hgvs_p": "p.Asp543Asn",
"inheritance_mode": "AR,AD",
"pathogenic_score": 0,
"score": -12,
"transcript": "NM_000578.4",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BA1",
"acmg_score": -12,
"allele_count_reference_population": 45696,
"alphamissense_prediction": "Benign",
"alphamissense_score": 0.0717,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.75,
"chr": "2",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": " susceptibility to,Buruli ulcer,Cystic fibrosis",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.0014781057834625244,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 550,
"aa_ref": "D",
"aa_start": 543,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3608,
"cdna_start": 1723,
"cds_end": null,
"cds_length": 1653,
"cds_start": 1627,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "NM_000578.4",
"gene_hgnc_id": 10907,
"gene_symbol": "SLC11A1",
"hgvs_c": "c.1627G>A",
"hgvs_p": "p.Asp543Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000233202.11",
"protein_coding": true,
"protein_id": "NP_000569.3",
"strand": true,
"transcript": "NM_000578.4",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 550,
"aa_ref": "D",
"aa_start": 543,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 3608,
"cdna_start": 1723,
"cds_end": null,
"cds_length": 1653,
"cds_start": 1627,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "ENST00000233202.11",
"gene_hgnc_id": 10907,
"gene_symbol": "SLC11A1",
"hgvs_c": "c.1627G>A",
"hgvs_p": "p.Asp543Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_000578.4",
"protein_coding": true,
"protein_id": "ENSP00000233202.6",
"strand": true,
"transcript": "ENST00000233202.11",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 2136,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 16,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000354352.9",
"gene_hgnc_id": 10907,
"gene_symbol": "SLC11A1",
"hgvs_c": "n.*1209G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000346320.5",
"strand": true,
"transcript": "ENST00000354352.9",
"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": 5772,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 13,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000468221.5",
"gene_hgnc_id": 10907,
"gene_symbol": "SLC11A1",
"hgvs_c": "n.4754G>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": "ENST00000468221.5",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 2136,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 16,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000354352.9",
"gene_hgnc_id": 10907,
"gene_symbol": "SLC11A1",
"hgvs_c": "n.*1209G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000346320.5",
"strand": true,
"transcript": "ENST00000354352.9",
"transcript_support_level": 1
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 514,
"aa_ref": "D",
"aa_start": 507,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3485,
"cdna_start": 1603,
"cds_end": null,
"cds_length": 1545,
"cds_start": 1519,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "ENST00000868333.1",
"gene_hgnc_id": 10907,
"gene_symbol": "SLC11A1",
"hgvs_c": "c.1519G>A",
"hgvs_p": "p.Asp507Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000538392.1",
"strand": true,
"transcript": "ENST00000868333.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 509,
"aa_ref": "D",
"aa_start": 502,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2045,
"cdna_start": 1741,
"cds_end": null,
"cds_length": 1530,
"cds_start": 1504,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "ENST00000868334.1",
"gene_hgnc_id": 10907,
"gene_symbol": "SLC11A1",
"hgvs_c": "c.1504G>A",
"hgvs_p": "p.Asp502Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000538393.1",
"strand": true,
"transcript": "ENST00000868334.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 500,
"aa_ref": "D",
"aa_start": 493,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1879,
"cdna_start": 1581,
"cds_end": null,
"cds_length": 1503,
"cds_start": 1477,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "ENST00000868335.1",
"gene_hgnc_id": 10907,
"gene_symbol": "SLC11A1",
"hgvs_c": "c.1477G>A",
"hgvs_p": "p.Asp493Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000538394.1",
"strand": true,
"transcript": "ENST00000868335.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 497,
"aa_ref": "D",
"aa_start": 490,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1888,
"cdna_start": 1604,
"cds_end": null,
"cds_length": 1494,
"cds_start": 1468,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "ENST00000965609.1",
"gene_hgnc_id": 10907,
"gene_symbol": "SLC11A1",
"hgvs_c": "c.1468G>A",
"hgvs_p": "p.Asp490Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000635668.1",
"strand": true,
"transcript": "ENST00000965609.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 469,
"aa_ref": "D",
"aa_start": 462,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1845,
"cdna_start": 1561,
"cds_end": null,
"cds_length": 1410,
"cds_start": 1384,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "ENST00000965608.1",
"gene_hgnc_id": 10907,
"gene_symbol": "SLC11A1",
"hgvs_c": "c.1384G>A",
"hgvs_p": "p.Asp462Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000635667.1",
"strand": true,
"transcript": "ENST00000965608.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 427,
"aa_ref": "D",
"aa_start": 420,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1630,
"cdna_start": 1326,
"cds_end": null,
"cds_length": 1284,
"cds_start": 1258,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000868336.1",
"gene_hgnc_id": 10907,
"gene_symbol": "SLC11A1",
"hgvs_c": "c.1258G>A",
"hgvs_p": "p.Asp420Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000538395.1",
"strand": true,
"transcript": "ENST00000868336.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 483,
"aa_ref": "D",
"aa_start": 476,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3465,
"cdna_start": 1580,
"cds_end": null,
"cds_length": 1452,
"cds_start": 1426,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "XM_005246793.5",
"gene_hgnc_id": 10907,
"gene_symbol": "SLC11A1",
"hgvs_c": "c.1426G>A",
"hgvs_p": "p.Asp476Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_005246850.1",
"strand": true,
"transcript": "XM_005246793.5",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 483,
"aa_ref": "D",
"aa_start": 476,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3450,
"cdna_start": 1565,
"cds_end": null,
"cds_length": 1452,
"cds_start": 1426,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "XM_017004766.3",
"gene_hgnc_id": 10907,
"gene_symbol": "SLC11A1",
"hgvs_c": "c.1426G>A",
"hgvs_p": "p.Asp476Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016860255.1",
"strand": true,
"transcript": "XM_017004766.3",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 432,
"aa_ref": "D",
"aa_start": 425,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3158,
"cdna_start": 1273,
"cds_end": null,
"cds_length": 1299,
"cds_start": 1273,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "XM_047445573.1",
"gene_hgnc_id": 10907,
"gene_symbol": "SLC11A1",
"hgvs_c": "c.1273G>A",
"hgvs_p": "p.Asp425Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047301529.1",
"strand": true,
"transcript": "XM_047445573.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 401,
"aa_ref": "D",
"aa_start": 394,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3342,
"cdna_start": 1457,
"cds_end": null,
"cds_length": 1206,
"cds_start": 1180,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "XM_006712711.5",
"gene_hgnc_id": 10907,
"gene_symbol": "SLC11A1",
"hgvs_c": "c.1180G>A",
"hgvs_p": "p.Asp394Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_006712774.1",
"strand": true,
"transcript": "XM_006712711.5",
"transcript_support_level": null
},
{
"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": 2548,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 14,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000465984.5",
"gene_hgnc_id": 10907,
"gene_symbol": "SLC11A1",
"hgvs_c": "n.2103G>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": "ENST00000465984.5",
"transcript_support_level": 2
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs17235409",
"effect": "missense_variant",
"frequency_reference_population": 0.028392661,
"gene_hgnc_id": 10907,
"gene_symbol": "SLC11A1",
"gnomad_exomes_ac": 39430,
"gnomad_exomes_af": 0.0270601,
"gnomad_exomes_homalt": 1109,
"gnomad_genomes_ac": 6266,
"gnomad_genomes_af": 0.0411414,
"gnomad_genomes_homalt": 195,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 1304,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "Buruli ulcer, susceptibility to|Cystic fibrosis",
"phylop100way_prediction": "Benign",
"phylop100way_score": -0.624,
"pos": 218395009,
"ref": "G",
"revel_prediction": "Benign",
"revel_score": 0.005,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_000578.4"
}
]
}