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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: 14-102929439-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=14&pos=102929439&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PVS1",
"PM2",
"PP5_Moderate"
],
"effects": [
"stop_gained"
],
"gene_symbol": "AMN",
"hgnc_id": 14604,
"hgvs_c": "c.663G>A",
"hgvs_p": "p.Trp221*",
"inheritance_mode": "AR",
"pathogenic_score": 12,
"score": 12,
"transcript": "NM_030943.4",
"verdict": "Pathogenic"
}
],
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5_Moderate",
"acmg_score": 12,
"allele_count_reference_population": 0,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.31,
"chr": "14",
"clinvar_classification": "Pathogenic",
"clinvar_disease": "Imerslund-Grasbeck syndrome",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "P:1",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.3100000023841858,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 453,
"aa_ref": "W",
"aa_start": 221,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1550,
"cdna_start": 689,
"cds_end": null,
"cds_length": 1362,
"cds_start": 663,
"consequences": [
"stop_gained"
],
"exon_count": 12,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "NM_030943.4",
"gene_hgnc_id": 14604,
"gene_symbol": "AMN",
"hgvs_c": "c.663G>A",
"hgvs_p": "p.Trp221*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000299155.10",
"protein_coding": true,
"protein_id": "NP_112205.2",
"strand": true,
"transcript": "NM_030943.4",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 453,
"aa_ref": "W",
"aa_start": 221,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 1550,
"cdna_start": 689,
"cds_end": null,
"cds_length": 1362,
"cds_start": 663,
"consequences": [
"stop_gained"
],
"exon_count": 12,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000299155.10",
"gene_hgnc_id": 14604,
"gene_symbol": "AMN",
"hgvs_c": "c.663G>A",
"hgvs_p": "p.Trp221*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_030943.4",
"protein_coding": true,
"protein_id": "ENSP00000299155.6",
"strand": true,
"transcript": "ENST00000299155.10",
"transcript_support_level": 1
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 434,
"aa_ref": "W",
"aa_start": 202,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1482,
"cdna_start": 622,
"cds_end": null,
"cds_length": 1305,
"cds_start": 606,
"consequences": [
"stop_gained"
],
"exon_count": 12,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000872999.1",
"gene_hgnc_id": 14604,
"gene_symbol": "AMN",
"hgvs_c": "c.606G>A",
"hgvs_p": "p.Trp202*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000543058.1",
"strand": true,
"transcript": "ENST00000872999.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 399,
"aa_ref": "W",
"aa_start": 167,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1569,
"cdna_start": 708,
"cds_end": null,
"cds_length": 1200,
"cds_start": 501,
"consequences": [
"stop_gained"
],
"exon_count": 12,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "NM_001425246.1",
"gene_hgnc_id": 14604,
"gene_symbol": "AMN",
"hgvs_c": "c.501G>A",
"hgvs_p": "p.Trp167*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001412175.1",
"strand": true,
"transcript": "NM_001425246.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 105,
"aa_ref": "W",
"aa_start": 94,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 320,
"cdna_start": 284,
"cds_end": null,
"cds_length": 318,
"cds_start": 282,
"consequences": [
"stop_gained"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000559525.1",
"gene_hgnc_id": 14604,
"gene_symbol": "AMN",
"hgvs_c": "c.282G>A",
"hgvs_p": "p.Trp94*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000453786.1",
"strand": true,
"transcript": "ENST00000559525.1",
"transcript_support_level": 3
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 399,
"aa_ref": "W",
"aa_start": 167,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1942,
"cdna_start": 1081,
"cds_end": null,
"cds_length": 1200,
"cds_start": 501,
"consequences": [
"stop_gained"
],
"exon_count": 12,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "XM_011537203.4",
"gene_hgnc_id": 14604,
"gene_symbol": "AMN",
"hgvs_c": "c.501G>A",
"hgvs_p": "p.Trp167*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011535505.1",
"strand": true,
"transcript": "XM_011537203.4",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 129,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 393,
"cdna_start": null,
"cds_end": null,
"cds_length": 391,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000559789.1",
"gene_hgnc_id": 14604,
"gene_symbol": "AMN",
"hgvs_c": "c.124+484G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000452831.1",
"strand": true,
"transcript": "ENST00000559789.1",
"transcript_support_level": 3
},
{
"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": 2269,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 11,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000541086.5",
"gene_hgnc_id": 14604,
"gene_symbol": "AMN",
"hgvs_c": "n.1409G>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": "ENST00000541086.5",
"transcript_support_level": 2
},
{
"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": 2772,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 9,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000558590.1",
"gene_hgnc_id": 14604,
"gene_symbol": "AMN",
"hgvs_c": "n.626G>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": "ENST00000558590.1",
"transcript_support_level": 2
},
{
"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": 470,
"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": "ENST00000559442.1",
"gene_hgnc_id": 14604,
"gene_symbol": "AMN",
"hgvs_c": "n.434G>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": "ENST00000559442.1",
"transcript_support_level": 2
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs386834174",
"effect": "stop_gained",
"frequency_reference_population": null,
"gene_hgnc_id": 14604,
"gene_symbol": "AMN",
"gnomad_exomes_ac": 0,
"gnomad_exomes_af": 0,
"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": "Imerslund-Grasbeck syndrome",
"phylop100way_prediction": "Benign",
"phylop100way_score": 1.369,
"pos": 102929439,
"ref": "G",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.05000000074505806,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.05,
"transcript": "NM_030943.4"
}
]
}