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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: 5-33989398-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=33989398&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 33989398,
"ref": "C",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000335606.11",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AMACR",
"gene_hgnc_id": 451,
"hgvs_c": "c.844G>C",
"hgvs_p": "p.Glu282Gln",
"transcript": "NM_014324.6",
"protein_id": "NP_055139.4",
"transcript_support_level": null,
"aa_start": 282,
"aa_end": null,
"aa_length": 382,
"cds_start": 844,
"cds_end": null,
"cds_length": 1149,
"cdna_start": 875,
"cdna_end": null,
"cdna_length": 4108,
"mane_select": "ENST00000335606.11",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AMACR",
"gene_hgnc_id": 451,
"hgvs_c": "c.844G>C",
"hgvs_p": "p.Glu282Gln",
"transcript": "ENST00000335606.11",
"protein_id": "ENSP00000334424.6",
"transcript_support_level": 1,
"aa_start": 282,
"aa_end": null,
"aa_length": 382,
"cds_start": 844,
"cds_end": null,
"cds_length": 1149,
"cdna_start": 875,
"cdna_end": null,
"cdna_length": 4108,
"mane_select": "NM_014324.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AMACR",
"gene_hgnc_id": 451,
"hgvs_c": "c.844G>C",
"hgvs_p": "p.Glu282Gln",
"transcript": "ENST00000382085.7",
"protein_id": "ENSP00000371517.3",
"transcript_support_level": 1,
"aa_start": 282,
"aa_end": null,
"aa_length": 394,
"cds_start": 844,
"cds_end": null,
"cds_length": 1185,
"cdna_start": 853,
"cdna_end": null,
"cdna_length": 1195,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "C1QTNF3-AMACR",
"gene_hgnc_id": 49198,
"hgvs_c": "n.*270G>C",
"hgvs_p": null,
"transcript": "ENST00000382079.3",
"protein_id": "ENSP00000371511.3",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3424,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AMACR",
"gene_hgnc_id": 451,
"hgvs_c": "n.*166G>C",
"hgvs_p": null,
"transcript": "ENST00000506639.5",
"protein_id": "ENSP00000427227.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2182,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AMACR",
"gene_hgnc_id": 451,
"hgvs_c": "n.738G>C",
"hgvs_p": null,
"transcript": "ENST00000514195.1",
"protein_id": null,
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2052,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AMACR",
"gene_hgnc_id": 451,
"hgvs_c": "c.*86G>C",
"hgvs_p": null,
"transcript": "ENST00000382072.6",
"protein_id": "ENSP00000371504.2",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 198,
"cds_start": -4,
"cds_end": null,
"cds_length": 597,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2919,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "C1QTNF3-AMACR",
"gene_hgnc_id": 49198,
"hgvs_c": "n.*270G>C",
"hgvs_p": null,
"transcript": "ENST00000382079.3",
"protein_id": "ENSP00000371511.3",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3424,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AMACR",
"gene_hgnc_id": 451,
"hgvs_c": "n.*166G>C",
"hgvs_p": null,
"transcript": "ENST00000506639.5",
"protein_id": "ENSP00000427227.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2182,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AMACR",
"gene_hgnc_id": 451,
"hgvs_c": "c.844G>C",
"hgvs_p": "p.Glu282Gln",
"transcript": "NM_001167595.2",
"protein_id": "NP_001161067.1",
"transcript_support_level": null,
"aa_start": 282,
"aa_end": null,
"aa_length": 394,
"cds_start": 844,
"cds_end": null,
"cds_length": 1185,
"cdna_start": 875,
"cdna_end": null,
"cdna_length": 2538,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AMACR",
"gene_hgnc_id": 451,
"hgvs_c": "c.799G>C",
"hgvs_p": "p.Glu267Gln",
"transcript": "ENST00000502637.5",
"protein_id": "ENSP00000424351.1",
"transcript_support_level": 5,
"aa_start": 267,
"aa_end": null,
"aa_length": 367,
"cds_start": 799,
"cds_end": null,
"cds_length": 1104,
"cdna_start": 884,
"cdna_end": null,
"cdna_length": 1598,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "C1QTNF3-AMACR",
"gene_hgnc_id": 49198,
"hgvs_c": "n.1200G>C",
"hgvs_p": null,
"transcript": "NR_037951.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3612,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AMACR",
"gene_hgnc_id": 451,
"hgvs_c": "c.*86G>C",
"hgvs_p": null,
"transcript": "NM_203382.3",
"protein_id": "NP_976316.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 198,
"cds_start": -4,
"cds_end": null,
"cds_length": 597,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3947,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "AMACR",
"gene_hgnc_id": 451,
"dbsnp": "rs181341030",
"frequency_reference_population": 0.00023664797,
"hom_count_reference_population": 5,
"allele_count_reference_population": 382,
"gnomad_exomes_af": 0.00023121,
"gnomad_genomes_af": 0.000288831,
"gnomad_exomes_ac": 338,
"gnomad_genomes_ac": 44,
"gnomad_exomes_homalt": 5,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.012740343809127808,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.377,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.1175,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.12,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 7.611,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -9,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6,BS2",
"acmg_by_gene": [
{
"score": -9,
"benign_score": 9,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000335606.11",
"gene_symbol": "AMACR",
"hgnc_id": 451,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.844G>C",
"hgvs_p": "p.Glu282Gln"
},
{
"score": -9,
"benign_score": 9,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000382079.3",
"gene_symbol": "C1QTNF3-AMACR",
"hgnc_id": 49198,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.*270G>C",
"hgvs_p": null
}
],
"clinvar_disease": "AMACR-related disorder,Alpha-methylacyl-CoA racemase deficiency,Congenital bile acid synthesis defect 4,Mitochondrial complex I deficiency,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:3 LB:3",
"phenotype_combined": "Mitochondrial complex I deficiency|not specified|Alpha-methylacyl-CoA racemase deficiency;Congenital bile acid synthesis defect 4|Alpha-methylacyl-CoA racemase deficiency|AMACR-related disorder",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}