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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: 10-70600663-T-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=10&pos=70600663&ref=T&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "10",
"pos": 70600663,
"ref": "T",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "NM_005041.6",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRF1",
"gene_hgnc_id": 9360,
"hgvs_c": "c.240A>T",
"hgvs_p": "p.Leu80Leu",
"transcript": "NM_001083116.3",
"protein_id": "NP_001076585.1",
"transcript_support_level": null,
"aa_start": 80,
"aa_end": null,
"aa_length": 555,
"cds_start": 240,
"cds_end": null,
"cds_length": 1668,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000441259.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001083116.3"
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRF1",
"gene_hgnc_id": 9360,
"hgvs_c": "c.240A>T",
"hgvs_p": "p.Leu80Leu",
"transcript": "ENST00000441259.2",
"protein_id": "ENSP00000398568.1",
"transcript_support_level": 5,
"aa_start": 80,
"aa_end": null,
"aa_length": 555,
"cds_start": 240,
"cds_end": null,
"cds_length": 1668,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001083116.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000441259.2"
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRF1",
"gene_hgnc_id": 9360,
"hgvs_c": "c.240A>T",
"hgvs_p": "p.Leu80Leu",
"transcript": "ENST00000373209.2",
"protein_id": "ENSP00000362305.1",
"transcript_support_level": 1,
"aa_start": 80,
"aa_end": null,
"aa_length": 555,
"cds_start": 240,
"cds_end": null,
"cds_length": 1668,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000373209.2"
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRF1",
"gene_hgnc_id": 9360,
"hgvs_c": "c.240A>T",
"hgvs_p": "p.Leu80Leu",
"transcript": "NM_005041.6",
"protein_id": "NP_005032.2",
"transcript_support_level": null,
"aa_start": 80,
"aa_end": null,
"aa_length": 555,
"cds_start": 240,
"cds_end": null,
"cds_length": 1668,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_005041.6"
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRF1",
"gene_hgnc_id": 9360,
"hgvs_c": "c.240A>T",
"hgvs_p": "p.Leu80Leu",
"transcript": "ENST00000862973.1",
"protein_id": "ENSP00000533032.1",
"transcript_support_level": null,
"aa_start": 80,
"aa_end": null,
"aa_length": 555,
"cds_start": 240,
"cds_end": null,
"cds_length": 1668,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000862973.1"
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRF1",
"gene_hgnc_id": 9360,
"hgvs_c": "c.240A>T",
"hgvs_p": "p.Leu80Leu",
"transcript": "ENST00000862974.1",
"protein_id": "ENSP00000533033.1",
"transcript_support_level": null,
"aa_start": 80,
"aa_end": null,
"aa_length": 555,
"cds_start": 240,
"cds_end": null,
"cds_length": 1668,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000862974.1"
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRF1",
"gene_hgnc_id": 9360,
"hgvs_c": "c.240A>T",
"hgvs_p": "p.Leu80Leu",
"transcript": "ENST00000945922.1",
"protein_id": "ENSP00000615981.1",
"transcript_support_level": null,
"aa_start": 80,
"aa_end": null,
"aa_length": 555,
"cds_start": 240,
"cds_end": null,
"cds_length": 1668,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000945922.1"
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRF1",
"gene_hgnc_id": 9360,
"hgvs_c": "c.240A>T",
"hgvs_p": "p.Leu80Leu",
"transcript": "ENST00000638674.1",
"protein_id": "ENSP00000492048.1",
"transcript_support_level": 5,
"aa_start": 80,
"aa_end": null,
"aa_length": 232,
"cds_start": 240,
"cds_end": null,
"cds_length": 699,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000638674.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": 20,
"intron_rank_end": null,
"gene_symbol": "PALD1",
"gene_hgnc_id": 23530,
"hgvs_c": "c.*17+1579T>A",
"hgvs_p": null,
"transcript": "ENST00000697571.1",
"protein_id": "ENSP00000513342.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 865,
"cds_start": null,
"cds_end": null,
"cds_length": 2598,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000697571.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": 19,
"intron_rank_end": null,
"gene_symbol": "PALD1",
"gene_hgnc_id": 23530,
"hgvs_c": "c.*17+1579T>A",
"hgvs_p": null,
"transcript": "ENST00000697573.1",
"protein_id": "ENSP00000513344.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 813,
"cds_start": null,
"cds_end": null,
"cds_length": 2442,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000697573.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": 18,
"intron_rank_end": null,
"gene_symbol": "PALD1",
"gene_hgnc_id": 23530,
"hgvs_c": "c.2250+36144T>A",
"hgvs_p": null,
"transcript": "ENST00000697572.1",
"protein_id": "ENSP00000513343.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 763,
"cds_start": null,
"cds_end": null,
"cds_length": 2292,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000697572.1"
},
{
"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": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PRF1",
"gene_hgnc_id": 9360,
"hgvs_c": "n.97+1982A>T",
"hgvs_p": null,
"transcript": "ENST00000639390.1",
"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": "pseudogene",
"feature": "ENST00000639390.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": 20,
"intron_rank_end": null,
"gene_symbol": "PALD1",
"gene_hgnc_id": 23530,
"hgvs_c": "n.2919+1579T>A",
"hgvs_p": null,
"transcript": "ENST00000697577.1",
"protein_id": null,
"transcript_support_level": null,
"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": "pseudogene",
"feature": "ENST00000697577.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": 19,
"intron_rank_end": null,
"gene_symbol": "PALD1",
"gene_hgnc_id": 23530,
"hgvs_c": "n.2763+1579T>A",
"hgvs_p": null,
"transcript": "ENST00000697578.1",
"protein_id": null,
"transcript_support_level": null,
"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": "pseudogene",
"feature": "ENST00000697578.1"
}
],
"gene_symbol": "PRF1",
"gene_hgnc_id": 9360,
"dbsnp": "rs140752768",
"frequency_reference_population": 0.00012765457,
"hom_count_reference_population": 0,
"allele_count_reference_population": 206,
"gnomad_exomes_af": 0.0000677403,
"gnomad_genomes_af": 0.000702718,
"gnomad_exomes_ac": 99,
"gnomad_genomes_ac": 107,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.8500000238418579,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.85,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.651,
"phylop100way_prediction": "Benign",
"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": -7,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Moderate,BP7",
"acmg_by_gene": [
{
"score": -7,
"benign_score": 7,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Moderate",
"BP7"
],
"verdict": "Benign",
"transcript": "NM_005041.6",
"gene_symbol": "PRF1",
"hgnc_id": 9360,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "Unknown,AR",
"hgvs_c": "c.240A>T",
"hgvs_p": "p.Leu80Leu"
},
{
"score": -6,
"benign_score": 6,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Moderate"
],
"verdict": "Likely_benign",
"transcript": "ENST00000697571.1",
"gene_symbol": "PALD1",
"hgnc_id": 23530,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.*17+1579T>A",
"hgvs_p": null
}
],
"clinvar_disease": "Familial hemophagocytic lymphohistiocytosis 2",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "Familial hemophagocytic lymphohistiocytosis 2",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}