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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: 7-47795989-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=7&pos=47795989&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "7",
"pos": 47795989,
"ref": "G",
"alt": "A",
"effect": "splice_region_variant,synonymous_variant",
"transcript": "NM_138295.5",
"consequences": [
{
"aa_ref": "H",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 55,
"exon_rank_end": null,
"exon_count": 57,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD1L1",
"gene_hgnc_id": 18053,
"hgvs_c": "c.8355C>T",
"hgvs_p": "p.His2785His",
"transcript": "NM_138295.5",
"protein_id": "NP_612152.1",
"transcript_support_level": null,
"aa_start": 2785,
"aa_end": null,
"aa_length": 2849,
"cds_start": 8355,
"cds_end": null,
"cds_length": 8550,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000289672.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_138295.5"
},
{
"aa_ref": "H",
"aa_alt": "H",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 55,
"exon_rank_end": null,
"exon_count": 57,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD1L1",
"gene_hgnc_id": 18053,
"hgvs_c": "c.8355C>T",
"hgvs_p": "p.His2785His",
"transcript": "ENST00000289672.7",
"protein_id": "ENSP00000289672.2",
"transcript_support_level": 1,
"aa_start": 2785,
"aa_end": null,
"aa_length": 2849,
"cds_start": 8355,
"cds_end": null,
"cds_length": 8550,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_138295.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000289672.7"
},
{
"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": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PKD1L1-AS1",
"gene_hgnc_id": 21911,
"hgvs_c": "n.153+546G>A",
"hgvs_p": null,
"transcript": "ENST00000623971.3",
"protein_id": null,
"transcript_support_level": 1,
"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": "ENST00000623971.3"
},
{
"aa_ref": "H",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 55,
"exon_rank_end": null,
"exon_count": 58,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD1L1",
"gene_hgnc_id": 18053,
"hgvs_c": "c.8355C>T",
"hgvs_p": "p.His2785His",
"transcript": "ENST00000690269.1",
"protein_id": "ENSP00000510743.1",
"transcript_support_level": null,
"aa_start": 2785,
"aa_end": null,
"aa_length": 2861,
"cds_start": 8355,
"cds_end": null,
"cds_length": 8586,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000690269.1"
},
{
"aa_ref": "H",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 54,
"exon_rank_end": null,
"exon_count": 56,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD1L1",
"gene_hgnc_id": 18053,
"hgvs_c": "c.8187C>T",
"hgvs_p": "p.His2729His",
"transcript": "ENST00000685709.1",
"protein_id": "ENSP00000509540.1",
"transcript_support_level": null,
"aa_start": 2729,
"aa_end": null,
"aa_length": 2793,
"cds_start": 8187,
"cds_end": null,
"cds_length": 8382,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000685709.1"
},
{
"aa_ref": "H",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD1L1",
"gene_hgnc_id": 18053,
"hgvs_c": "c.1995C>T",
"hgvs_p": "p.His665His",
"transcript": "ENST00000686775.1",
"protein_id": "ENSP00000508550.1",
"transcript_support_level": null,
"aa_start": 665,
"aa_end": null,
"aa_length": 745,
"cds_start": 1995,
"cds_end": null,
"cds_length": 2238,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000686775.1"
},
{
"aa_ref": "H",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD1L1",
"gene_hgnc_id": 18053,
"hgvs_c": "c.987C>T",
"hgvs_p": "p.His329His",
"transcript": "ENST00000648482.1",
"protein_id": "ENSP00000496786.1",
"transcript_support_level": null,
"aa_start": 329,
"aa_end": null,
"aa_length": 435,
"cds_start": 987,
"cds_end": null,
"cds_length": 1308,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000648482.1"
},
{
"aa_ref": "H",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 56,
"exon_rank_end": null,
"exon_count": 59,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD1L1",
"gene_hgnc_id": 18053,
"hgvs_c": "c.8532C>T",
"hgvs_p": "p.His2844His",
"transcript": "XM_017011798.3",
"protein_id": "XP_016867287.1",
"transcript_support_level": null,
"aa_start": 2844,
"aa_end": null,
"aa_length": 2920,
"cds_start": 8532,
"cds_end": null,
"cds_length": 8763,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017011798.3"
},
{
"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": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PKD1L1-AS1",
"gene_hgnc_id": 21911,
"hgvs_c": "n.20+546G>A",
"hgvs_p": null,
"transcript": "ENST00000418326.3",
"protein_id": null,
"transcript_support_level": 4,
"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": "ENST00000418326.3"
},
{
"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": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PKD1L1-AS1",
"gene_hgnc_id": 21911,
"hgvs_c": "n.153+546G>A",
"hgvs_p": null,
"transcript": "NR_161268.1",
"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": "NR_161268.1"
},
{
"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": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PKD1L1-AS1",
"gene_hgnc_id": 21911,
"hgvs_c": "n.153+546G>A",
"hgvs_p": null,
"transcript": "NR_161269.1",
"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": "NR_161269.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD1L1",
"gene_hgnc_id": 18053,
"hgvs_c": "c.*82C>T",
"hgvs_p": null,
"transcript": "ENST00000433506.2",
"protein_id": "ENSP00000393466.2",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 315,
"cds_start": null,
"cds_end": null,
"cds_length": 950,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000433506.2"
}
],
"gene_symbol": "PKD1L1",
"gene_hgnc_id": 18053,
"dbsnp": "rs751054839",
"frequency_reference_population": 0.000054616863,
"hom_count_reference_population": 0,
"allele_count_reference_population": 88,
"gnomad_exomes_af": 0.0000527751,
"gnomad_genomes_af": 0.0000722724,
"gnomad_exomes_ac": 77,
"gnomad_genomes_ac": 11,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.9399999976158142,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.029999999329447746,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.94,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -2.059,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.11,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.0000627089106755083,
"dbscsnv_ada_prediction": "Benign",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -5,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Strong,BP7",
"acmg_by_gene": [
{
"score": -5,
"benign_score": 5,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP7"
],
"verdict": "Likely_benign",
"transcript": "NM_138295.5",
"gene_symbol": "PKD1L1",
"hgnc_id": 18053,
"effects": [
"splice_region_variant",
"synonymous_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.8355C>T",
"hgvs_p": "p.His2785His"
},
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "ENST00000623971.3",
"gene_symbol": "PKD1L1-AS1",
"hgnc_id": 21911,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.153+546G>A",
"hgvs_p": null
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}