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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: 7-47800736-GAGGCAGTCTT-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=7&pos=47800736&ref=GAGGCAGTCTT&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "7",
"pos": 47800736,
"ref": "GAGGCAGTCTT",
"alt": "G",
"effect": "frameshift_variant",
"transcript": "NM_138295.5",
"consequences": [
{
"aa_ref": "KDCL",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 54,
"exon_rank_end": null,
"exon_count": 57,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD1L1",
"gene_hgnc_id": 18053,
"hgvs_c": "c.8096_8105delAAGACTGCCT",
"hgvs_p": "p.Lys2699fs",
"transcript": "NM_138295.5",
"protein_id": "NP_612152.1",
"transcript_support_level": null,
"aa_start": 2699,
"aa_end": null,
"aa_length": 2849,
"cds_start": 8096,
"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": "KDCL",
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 54,
"exon_rank_end": null,
"exon_count": 57,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD1L1",
"gene_hgnc_id": 18053,
"hgvs_c": "c.8096_8105delAAGACTGCCT",
"hgvs_p": "p.Lys2699fs",
"transcript": "ENST00000289672.7",
"protein_id": "ENSP00000289672.2",
"transcript_support_level": 1,
"aa_start": 2699,
"aa_end": null,
"aa_length": 2849,
"cds_start": 8096,
"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+5294_153+5303delAGGCAGTCTT",
"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": "KDCL",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 54,
"exon_rank_end": null,
"exon_count": 58,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD1L1",
"gene_hgnc_id": 18053,
"hgvs_c": "c.8096_8105delAAGACTGCCT",
"hgvs_p": "p.Lys2699fs",
"transcript": "ENST00000690269.1",
"protein_id": "ENSP00000510743.1",
"transcript_support_level": null,
"aa_start": 2699,
"aa_end": null,
"aa_length": 2861,
"cds_start": 8096,
"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": "KDCL",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 53,
"exon_rank_end": null,
"exon_count": 56,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD1L1",
"gene_hgnc_id": 18053,
"hgvs_c": "c.7928_7937delAAGACTGCCT",
"hgvs_p": "p.Lys2643fs",
"transcript": "ENST00000685709.1",
"protein_id": "ENSP00000509540.1",
"transcript_support_level": null,
"aa_start": 2643,
"aa_end": null,
"aa_length": 2793,
"cds_start": 7928,
"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": "KDCL",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD1L1",
"gene_hgnc_id": 18053,
"hgvs_c": "c.1736_1745delAAGACTGCCT",
"hgvs_p": "p.Lys579fs",
"transcript": "ENST00000686775.1",
"protein_id": "ENSP00000508550.1",
"transcript_support_level": null,
"aa_start": 579,
"aa_end": null,
"aa_length": 745,
"cds_start": 1736,
"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": "KDCL",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD1L1",
"gene_hgnc_id": 18053,
"hgvs_c": "c.728_737delAAGACTGCCT",
"hgvs_p": "p.Lys243fs",
"transcript": "ENST00000648482.1",
"protein_id": "ENSP00000496786.1",
"transcript_support_level": null,
"aa_start": 243,
"aa_end": null,
"aa_length": 435,
"cds_start": 728,
"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": "KDCL",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD1L1",
"gene_hgnc_id": 18053,
"hgvs_c": "c.773_782delAAGACTGCCT",
"hgvs_p": "p.Lys258fs",
"transcript": "ENST00000433506.2",
"protein_id": "ENSP00000393466.2",
"transcript_support_level": 3,
"aa_start": 258,
"aa_end": null,
"aa_length": 315,
"cds_start": 773,
"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"
},
{
"aa_ref": "KDCL",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 55,
"exon_rank_end": null,
"exon_count": 59,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD1L1",
"gene_hgnc_id": 18053,
"hgvs_c": "c.8273_8282delAAGACTGCCT",
"hgvs_p": "p.Lys2758fs",
"transcript": "XM_017011798.3",
"protein_id": "XP_016867287.1",
"transcript_support_level": null,
"aa_start": 2758,
"aa_end": null,
"aa_length": 2920,
"cds_start": 8273,
"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+5294_20+5303delAGGCAGTCTT",
"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+5294_153+5303delAGGCAGTCTT",
"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+5294_153+5303delAGGCAGTCTT",
"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"
}
],
"gene_symbol": "PKD1L1",
"gene_hgnc_id": 18053,
"dbsnp": "rs1784643052",
"frequency_reference_population": 0.0000012390883,
"hom_count_reference_population": 0,
"allele_count_reference_population": 2,
"gnomad_exomes_af": 6.84045e-7,
"gnomad_genomes_af": 0.00000657039,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"splice_score_selected": null,
"splice_prediction_selected": null,
"splice_source_selected": null,
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 0.448,
"phylop100way_prediction": "Benign",
"spliceai_max_score": null,
"spliceai_max_prediction": null,
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 12,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5_Moderate",
"acmg_by_gene": [
{
"score": 12,
"benign_score": 0,
"pathogenic_score": 12,
"criteria": [
"PVS1",
"PM2",
"PP5_Moderate"
],
"verdict": "Pathogenic",
"transcript": "NM_138295.5",
"gene_symbol": "PKD1L1",
"hgnc_id": 18053,
"effects": [
"frameshift_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.8096_8105delAAGACTGCCT",
"hgvs_p": "p.Lys2699fs"
},
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP5_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000623971.3",
"gene_symbol": "PKD1L1-AS1",
"hgnc_id": 21911,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.153+5294_153+5303delAGGCAGTCTT",
"hgvs_p": null
}
],
"clinvar_disease": " 8, autosomal, visceral,Heterotaxy",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "P:1",
"phenotype_combined": "Heterotaxy, visceral, 8, autosomal",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}