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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: 5-33989459-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=33989459&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 4,
"criteria": [
"BP4_Strong"
],
"effects": [
"missense_variant"
],
"gene_symbol": "AMACR",
"hgnc_id": 451,
"hgvs_c": "c.783G>A",
"hgvs_p": "p.Met261Ile",
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -4,
"transcript": "NM_001167595.2",
"verdict": "Likely_benign"
},
{
"benign_score": 4,
"criteria": [
"BP4_Strong"
],
"effects": [
"non_coding_transcript_exon_variant"
],
"gene_symbol": "C1QTNF3-AMACR",
"hgnc_id": 49198,
"hgvs_c": "n.*209G>A",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 0,
"score": -4,
"transcript": "ENST00000382079.3",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Strong",
"acmg_score": -4,
"allele_count_reference_population": 190,
"alphamissense_prediction": null,
"alphamissense_score": 0.2133,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.7,
"chr": "5",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "AMACR-related disorder,Alpha-methylacyl-CoA racemase deficiency,Congenital bile acid synthesis defect 4,not provided",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:4",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.00673288106918335,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 382,
"aa_ref": "M",
"aa_start": 261,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4108,
"cdna_start": 814,
"cds_end": null,
"cds_length": 1149,
"cds_start": 783,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "NM_014324.6",
"gene_hgnc_id": 451,
"gene_symbol": "AMACR",
"hgvs_c": "c.783G>A",
"hgvs_p": "p.Met261Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000335606.11",
"protein_coding": true,
"protein_id": "NP_055139.4",
"strand": false,
"transcript": "NM_014324.6",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 382,
"aa_ref": "M",
"aa_start": 261,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 4108,
"cdna_start": 814,
"cds_end": null,
"cds_length": 1149,
"cds_start": 783,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000335606.11",
"gene_hgnc_id": 451,
"gene_symbol": "AMACR",
"hgvs_c": "c.783G>A",
"hgvs_p": "p.Met261Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_014324.6",
"protein_coding": true,
"protein_id": "ENSP00000334424.6",
"strand": false,
"transcript": "ENST00000335606.11",
"transcript_support_level": 1
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 394,
"aa_ref": "M",
"aa_start": 261,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1195,
"cdna_start": 792,
"cds_end": null,
"cds_length": 1185,
"cds_start": 783,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000382085.7",
"gene_hgnc_id": 451,
"gene_symbol": "AMACR",
"hgvs_c": "c.783G>A",
"hgvs_p": "p.Met261Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000371517.3",
"strand": false,
"transcript": "ENST00000382085.7",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 198,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2919,
"cdna_start": null,
"cds_end": null,
"cds_length": 597,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000382072.6",
"gene_hgnc_id": 451,
"gene_symbol": "AMACR",
"hgvs_c": "c.*25G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000371504.2",
"strand": false,
"transcript": "ENST00000382072.6",
"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": 3424,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 9,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000382079.3",
"gene_hgnc_id": 49198,
"gene_symbol": "C1QTNF3-AMACR",
"hgvs_c": "n.*209G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000371511.3",
"strand": false,
"transcript": "ENST00000382079.3",
"transcript_support_level": 2
},
{
"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": 2182,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000506639.5",
"gene_hgnc_id": 451,
"gene_symbol": "AMACR",
"hgvs_c": "n.*105G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000427227.1",
"strand": false,
"transcript": "ENST00000506639.5",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 2052,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000514195.1",
"gene_hgnc_id": 451,
"gene_symbol": "AMACR",
"hgvs_c": "n.677G>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": "ENST00000514195.1",
"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": 3424,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 9,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000382079.3",
"gene_hgnc_id": 49198,
"gene_symbol": "C1QTNF3-AMACR",
"hgvs_c": "n.*209G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000371511.3",
"strand": false,
"transcript": "ENST00000382079.3",
"transcript_support_level": 2
},
{
"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": 2182,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000506639.5",
"gene_hgnc_id": 451,
"gene_symbol": "AMACR",
"hgvs_c": "n.*105G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000427227.1",
"strand": false,
"transcript": "ENST00000506639.5",
"transcript_support_level": 1
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 394,
"aa_ref": "M",
"aa_start": 261,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2538,
"cdna_start": 814,
"cds_end": null,
"cds_length": 1185,
"cds_start": 783,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "NM_001167595.2",
"gene_hgnc_id": 451,
"gene_symbol": "AMACR",
"hgvs_c": "c.783G>A",
"hgvs_p": "p.Met261Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001161067.1",
"strand": false,
"transcript": "NM_001167595.2",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 367,
"aa_ref": "M",
"aa_start": 246,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1598,
"cdna_start": 823,
"cds_end": null,
"cds_length": 1104,
"cds_start": 738,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000502637.5",
"gene_hgnc_id": 451,
"gene_symbol": "AMACR",
"hgvs_c": "c.738G>A",
"hgvs_p": "p.Met246Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000424351.1",
"strand": false,
"transcript": "ENST00000502637.5",
"transcript_support_level": 5
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 266,
"aa_ref": "M",
"aa_start": 145,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1276,
"cdna_start": 467,
"cds_end": null,
"cds_length": 801,
"cds_start": 435,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000926930.1",
"gene_hgnc_id": 451,
"gene_symbol": "AMACR",
"hgvs_c": "c.435G>A",
"hgvs_p": "p.Met145Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000596989.1",
"strand": false,
"transcript": "ENST00000926930.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 198,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3947,
"cdna_start": null,
"cds_end": null,
"cds_length": 597,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "NM_203382.3",
"gene_hgnc_id": 451,
"gene_symbol": "AMACR",
"hgvs_c": "c.*25G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_976316.1",
"strand": false,
"transcript": "NM_203382.3",
"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": 3612,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 9,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "NR_037951.1",
"gene_hgnc_id": 49198,
"gene_symbol": "C1QTNF3-AMACR",
"hgvs_c": "n.1139G>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": "NR_037951.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs9282593",
"effect": "missense_variant",
"frequency_reference_population": 0.00011770522,
"gene_hgnc_id": 451,
"gene_symbol": "AMACR",
"gnomad_exomes_ac": 147,
"gnomad_exomes_af": 0.000100556,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 43,
"gnomad_genomes_af": 0.000282286,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "not provided|Alpha-methylacyl-CoA racemase deficiency;Congenital bile acid synthesis defect 4|Alpha-methylacyl-CoA racemase deficiency|AMACR-related disorder",
"phylop100way_prediction": "Benign",
"phylop100way_score": -0.244,
"pos": 33989459,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.026,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_001167595.2"
}
]
}