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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: 5-34007866-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=34007866&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 34007866,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000335606.11",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AMACR",
"gene_hgnc_id": 451,
"hgvs_c": "c.154T>C",
"hgvs_p": "p.Ser52Pro",
"transcript": "NM_014324.6",
"protein_id": "NP_055139.4",
"transcript_support_level": null,
"aa_start": 52,
"aa_end": null,
"aa_length": 382,
"cds_start": 154,
"cds_end": null,
"cds_length": 1149,
"cdna_start": 185,
"cdna_end": null,
"cdna_length": 4108,
"mane_select": "ENST00000335606.11",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "P",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AMACR",
"gene_hgnc_id": 451,
"hgvs_c": "c.154T>C",
"hgvs_p": "p.Ser52Pro",
"transcript": "ENST00000335606.11",
"protein_id": "ENSP00000334424.6",
"transcript_support_level": 1,
"aa_start": 52,
"aa_end": null,
"aa_length": 382,
"cds_start": 154,
"cds_end": null,
"cds_length": 1149,
"cdna_start": 185,
"cdna_end": null,
"cdna_length": 4108,
"mane_select": "NM_014324.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AMACR",
"gene_hgnc_id": 451,
"hgvs_c": "c.154T>C",
"hgvs_p": "p.Ser52Pro",
"transcript": "ENST00000382085.7",
"protein_id": "ENSP00000371517.3",
"transcript_support_level": 1,
"aa_start": 52,
"aa_end": null,
"aa_length": 394,
"cds_start": 154,
"cds_end": null,
"cds_length": 1185,
"cdna_start": 163,
"cdna_end": null,
"cdna_length": 1195,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "P",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000289791",
"gene_hgnc_id": null,
"hgvs_c": "c.154T>C",
"hgvs_p": "p.Ser52Pro",
"transcript": "ENST00000426255.6",
"protein_id": "ENSP00000476965.1",
"transcript_support_level": 2,
"aa_start": 52,
"aa_end": null,
"aa_length": 288,
"cds_start": 154,
"cds_end": null,
"cds_length": 867,
"cdna_start": 219,
"cdna_end": null,
"cdna_length": 1316,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000289791",
"gene_hgnc_id": null,
"hgvs_c": "c.154T>C",
"hgvs_p": "p.Ser52Pro",
"transcript": "ENST00000382068.3",
"protein_id": "ENSP00000477108.1",
"transcript_support_level": 1,
"aa_start": 52,
"aa_end": null,
"aa_length": 281,
"cds_start": 154,
"cds_end": null,
"cds_length": 846,
"cdna_start": 163,
"cdna_end": null,
"cdna_length": 862,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000289791",
"gene_hgnc_id": null,
"hgvs_c": "c.154T>C",
"hgvs_p": "p.Ser52Pro",
"transcript": "ENST00000512079.5",
"protein_id": "ENSP00000477411.1",
"transcript_support_level": 1,
"aa_start": 52,
"aa_end": null,
"aa_length": 260,
"cds_start": 154,
"cds_end": null,
"cds_length": 783,
"cdna_start": 163,
"cdna_end": null,
"cdna_length": 858,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AMACR",
"gene_hgnc_id": 451,
"hgvs_c": "c.154T>C",
"hgvs_p": "p.Ser52Pro",
"transcript": "ENST00000382072.6",
"protein_id": "ENSP00000371504.2",
"transcript_support_level": 1,
"aa_start": 52,
"aa_end": null,
"aa_length": 198,
"cds_start": 154,
"cds_end": null,
"cds_length": 597,
"cdna_start": 166,
"cdna_end": null,
"cdna_length": 2919,
"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": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AMACR",
"gene_hgnc_id": 451,
"hgvs_c": "n.154T>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": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AMACR",
"gene_hgnc_id": 451,
"hgvs_c": "n.166T>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": true,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "C1QTNF3-AMACR",
"gene_hgnc_id": 49198,
"hgvs_c": "n.690-1967T>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": "S",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AMACR",
"gene_hgnc_id": 451,
"hgvs_c": "c.154T>C",
"hgvs_p": "p.Ser52Pro",
"transcript": "NM_001167595.2",
"protein_id": "NP_001161067.1",
"transcript_support_level": null,
"aa_start": 52,
"aa_end": null,
"aa_length": 394,
"cds_start": 154,
"cds_end": null,
"cds_length": 1185,
"cdna_start": 185,
"cdna_end": null,
"cdna_length": 2538,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AMACR",
"gene_hgnc_id": 451,
"hgvs_c": "c.154T>C",
"hgvs_p": "p.Ser52Pro",
"transcript": "ENST00000502637.5",
"protein_id": "ENSP00000424351.1",
"transcript_support_level": 5,
"aa_start": 52,
"aa_end": null,
"aa_length": 367,
"cds_start": 154,
"cds_end": null,
"cds_length": 1104,
"cdna_start": 239,
"cdna_end": null,
"cdna_length": 1598,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AMACR",
"gene_hgnc_id": 451,
"hgvs_c": "c.154T>C",
"hgvs_p": "p.Ser52Pro",
"transcript": "NM_203382.3",
"protein_id": "NP_976316.1",
"transcript_support_level": null,
"aa_start": 52,
"aa_end": null,
"aa_length": 198,
"cds_start": 154,
"cds_end": null,
"cds_length": 597,
"cdna_start": 185,
"cdna_end": null,
"cdna_length": 3947,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "C1QTNF3-AMACR",
"gene_hgnc_id": 49198,
"hgvs_c": "n.765-1967T>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
}
],
"gene_symbol": "AMACR",
"gene_hgnc_id": 451,
"dbsnp": "rs121917814",
"frequency_reference_population": 0.0008360667,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1329,
"gnomad_exomes_af": 0.000877941,
"gnomad_genomes_af": 0.000440407,
"gnomad_exomes_ac": 1262,
"gnomad_genomes_ac": 67,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.3762824535369873,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.741,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.934,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.4,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 6.119,
"phylop100way_prediction": "Uncertain_significance",
"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": 8,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PP3,PP5_Very_Strong,BP4",
"acmg_by_gene": [
{
"score": 8,
"benign_score": 1,
"pathogenic_score": 9,
"criteria": [
"PP3",
"PP5_Very_Strong",
"BP4"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000335606.11",
"gene_symbol": "AMACR",
"hgnc_id": 451,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.154T>C",
"hgvs_p": "p.Ser52Pro"
},
{
"score": 8,
"benign_score": 1,
"pathogenic_score": 9,
"criteria": [
"PP3",
"PP5_Very_Strong",
"BP4"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000426255.6",
"gene_symbol": "ENSG00000289791",
"hgnc_id": null,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.154T>C",
"hgvs_p": "p.Ser52Pro"
},
{
"score": 8,
"benign_score": 1,
"pathogenic_score": 9,
"criteria": [
"PP3",
"PP5_Very_Strong",
"BP4"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000382079.3",
"gene_symbol": "C1QTNF3-AMACR",
"hgnc_id": 49198,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.690-1967T>C",
"hgvs_p": null
}
],
"clinvar_disease": "AMACR-related disorder,Alpha-methylacyl-CoA racemase deficiency,Congenital bile acid synthesis defect 4,Inborn genetic diseases,not provided",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:6 LP:2",
"phenotype_combined": "Congenital bile acid synthesis defect 4|Alpha-methylacyl-CoA racemase deficiency|not provided|AMACR-related disorder|Inborn genetic diseases",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}