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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: 19-8490362-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=8490362&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 8490362,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_032152.5",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRAM1",
"gene_hgnc_id": 30091,
"hgvs_c": "c.1951G>A",
"hgvs_p": "p.Val651Met",
"transcript": "NM_032152.5",
"protein_id": "NP_115528.4",
"transcript_support_level": null,
"aa_start": 651,
"aa_end": null,
"aa_length": 670,
"cds_start": 1951,
"cds_end": null,
"cds_length": 2013,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000423345.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_032152.5"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRAM1",
"gene_hgnc_id": 30091,
"hgvs_c": "c.1951G>A",
"hgvs_p": "p.Val651Met",
"transcript": "ENST00000423345.5",
"protein_id": "ENSP00000408342.2",
"transcript_support_level": 1,
"aa_start": 651,
"aa_end": null,
"aa_length": 670,
"cds_start": 1951,
"cds_end": null,
"cds_length": 2013,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_032152.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000423345.5"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRAM1",
"gene_hgnc_id": 30091,
"hgvs_c": "c.1963G>A",
"hgvs_p": "p.Val655Met",
"transcript": "ENST00000880309.1",
"protein_id": "ENSP00000550368.1",
"transcript_support_level": null,
"aa_start": 655,
"aa_end": null,
"aa_length": 674,
"cds_start": 1963,
"cds_end": null,
"cds_length": 2025,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000880309.1"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRAM1",
"gene_hgnc_id": 30091,
"hgvs_c": "c.1957G>A",
"hgvs_p": "p.Val653Met",
"transcript": "XM_011528352.3",
"protein_id": "XP_011526654.1",
"transcript_support_level": null,
"aa_start": 653,
"aa_end": null,
"aa_length": 709,
"cds_start": 1957,
"cds_end": null,
"cds_length": 2130,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011528352.3"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRAM1",
"gene_hgnc_id": 30091,
"hgvs_c": "c.1951G>A",
"hgvs_p": "p.Val651Met",
"transcript": "XM_005272502.3",
"protein_id": "XP_005272559.1",
"transcript_support_level": null,
"aa_start": 651,
"aa_end": null,
"aa_length": 707,
"cds_start": 1951,
"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": "XM_005272502.3"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRAM1",
"gene_hgnc_id": 30091,
"hgvs_c": "c.1957G>A",
"hgvs_p": "p.Val653Met",
"transcript": "XM_011528353.3",
"protein_id": "XP_011526655.1",
"transcript_support_level": null,
"aa_start": 653,
"aa_end": null,
"aa_length": 672,
"cds_start": 1957,
"cds_end": null,
"cds_length": 2019,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011528353.3"
},
{
"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": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRAM1",
"gene_hgnc_id": 30091,
"hgvs_c": "n.1241G>A",
"hgvs_p": null,
"transcript": "ENST00000594696.1",
"protein_id": null,
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000594696.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRAM1",
"gene_hgnc_id": 30091,
"hgvs_c": "n.327G>A",
"hgvs_p": null,
"transcript": "ENST00000599698.5",
"protein_id": null,
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000599698.5"
}
],
"gene_symbol": "PRAM1",
"gene_hgnc_id": 30091,
"dbsnp": "rs1441408390",
"frequency_reference_population": 0.0000034210068,
"hom_count_reference_population": 0,
"allele_count_reference_population": 5,
"gnomad_exomes_af": 0.00000342101,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 5,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.6225233674049377,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.07999999821186066,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.145,
"revel_prediction": "Benign",
"alphamissense_score": 0.8763,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": -0.35,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.26,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.08,
"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": 2,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "NM_032152.5",
"gene_symbol": "PRAM1",
"hgnc_id": 30091,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1951G>A",
"hgvs_p": "p.Val651Met"
}
],
"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
}