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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: 6-105278398-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=105278398&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "6",
"pos": 105278398,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_002726.5",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PREP",
"gene_hgnc_id": 9358,
"hgvs_c": "c.1879G>A",
"hgvs_p": "p.Asp627Asn",
"transcript": "NM_002726.5",
"protein_id": "NP_002717.3",
"transcript_support_level": null,
"aa_start": 627,
"aa_end": null,
"aa_length": 710,
"cds_start": 1879,
"cds_end": null,
"cds_length": 2133,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000652536.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_002726.5"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PREP",
"gene_hgnc_id": 9358,
"hgvs_c": "c.1879G>A",
"hgvs_p": "p.Asp627Asn",
"transcript": "ENST00000652536.2",
"protein_id": "ENSP00000499089.1",
"transcript_support_level": null,
"aa_start": 627,
"aa_end": null,
"aa_length": 710,
"cds_start": 1879,
"cds_end": null,
"cds_length": 2133,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_002726.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000652536.2"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PREP",
"gene_hgnc_id": 9358,
"hgvs_c": "c.1681G>A",
"hgvs_p": "p.Asp561Asn",
"transcript": "ENST00000369110.8",
"protein_id": "ENSP00000358106.4",
"transcript_support_level": 1,
"aa_start": 561,
"aa_end": null,
"aa_length": 644,
"cds_start": 1681,
"cds_end": null,
"cds_length": 1935,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000369110.8"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PREP",
"gene_hgnc_id": 9358,
"hgvs_c": "c.1945G>A",
"hgvs_p": "p.Asp649Asn",
"transcript": "ENST00000969640.1",
"protein_id": "ENSP00000639699.1",
"transcript_support_level": null,
"aa_start": 649,
"aa_end": null,
"aa_length": 732,
"cds_start": 1945,
"cds_end": null,
"cds_length": 2199,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000969640.1"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PREP",
"gene_hgnc_id": 9358,
"hgvs_c": "c.1870G>A",
"hgvs_p": "p.Asp624Asn",
"transcript": "ENST00000910823.1",
"protein_id": "ENSP00000580882.1",
"transcript_support_level": null,
"aa_start": 624,
"aa_end": null,
"aa_length": 707,
"cds_start": 1870,
"cds_end": null,
"cds_length": 2124,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000910823.1"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PREP",
"gene_hgnc_id": 9358,
"hgvs_c": "c.1870G>A",
"hgvs_p": "p.Asp624Asn",
"transcript": "ENST00000910825.1",
"protein_id": "ENSP00000580884.1",
"transcript_support_level": null,
"aa_start": 624,
"aa_end": null,
"aa_length": 707,
"cds_start": 1870,
"cds_end": null,
"cds_length": 2124,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000910825.1"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PREP",
"gene_hgnc_id": 9358,
"hgvs_c": "c.1828G>A",
"hgvs_p": "p.Asp610Asn",
"transcript": "ENST00000910821.1",
"protein_id": "ENSP00000580880.1",
"transcript_support_level": null,
"aa_start": 610,
"aa_end": null,
"aa_length": 693,
"cds_start": 1828,
"cds_end": null,
"cds_length": 2082,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000910821.1"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PREP",
"gene_hgnc_id": 9358,
"hgvs_c": "c.1687G>A",
"hgvs_p": "p.Asp563Asn",
"transcript": "ENST00000910822.1",
"protein_id": "ENSP00000580881.1",
"transcript_support_level": null,
"aa_start": 563,
"aa_end": null,
"aa_length": 646,
"cds_start": 1687,
"cds_end": null,
"cds_length": 1941,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000910822.1"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PREP",
"gene_hgnc_id": 9358,
"hgvs_c": "c.1678G>A",
"hgvs_p": "p.Asp560Asn",
"transcript": "ENST00000920421.1",
"protein_id": "ENSP00000590480.1",
"transcript_support_level": null,
"aa_start": 560,
"aa_end": null,
"aa_length": 643,
"cds_start": 1678,
"cds_end": null,
"cds_length": 1932,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000920421.1"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PREP",
"gene_hgnc_id": 9358,
"hgvs_c": "c.1636G>A",
"hgvs_p": "p.Asp546Asn",
"transcript": "ENST00000910824.1",
"protein_id": "ENSP00000580883.1",
"transcript_support_level": null,
"aa_start": 546,
"aa_end": null,
"aa_length": 629,
"cds_start": 1636,
"cds_end": null,
"cds_length": 1890,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000910824.1"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PREP",
"gene_hgnc_id": 9358,
"hgvs_c": "c.1495G>A",
"hgvs_p": "p.Asp499Asn",
"transcript": "ENST00000969641.1",
"protein_id": "ENSP00000639700.1",
"transcript_support_level": null,
"aa_start": 499,
"aa_end": null,
"aa_length": 582,
"cds_start": 1495,
"cds_end": null,
"cds_length": 1749,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000969641.1"
}
],
"gene_symbol": "PREP",
"gene_hgnc_id": 9358,
"dbsnp": null,
"frequency_reference_population": 0.000002052576,
"hom_count_reference_population": 0,
"allele_count_reference_population": 3,
"gnomad_exomes_af": 0.00000205258,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 3,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.12960445880889893,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.125,
"revel_prediction": "Benign",
"alphamissense_score": 0.0749,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.62,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 7.568,
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_002726.5",
"gene_symbol": "PREP",
"hgnc_id": 9358,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1879G>A",
"hgvs_p": "p.Asp627Asn"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}