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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: 6-51619163-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=51619163&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "6",
"pos": 51619163,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_138694.4",
"consequences": [
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 67,
"exon_rank_end": null,
"exon_count": 67,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"hgvs_c": "c.12143A>G",
"hgvs_p": "p.Gln4048Arg",
"transcript": "NM_138694.4",
"protein_id": "NP_619639.3",
"transcript_support_level": null,
"aa_start": 4048,
"aa_end": null,
"aa_length": 4074,
"cds_start": 12143,
"cds_end": null,
"cds_length": 12225,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000371117.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_138694.4"
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 67,
"exon_rank_end": null,
"exon_count": 67,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"hgvs_c": "c.12143A>G",
"hgvs_p": "p.Gln4048Arg",
"transcript": "ENST00000371117.8",
"protein_id": "ENSP00000360158.3",
"transcript_support_level": 1,
"aa_start": 4048,
"aa_end": null,
"aa_length": 4074,
"cds_start": 12143,
"cds_end": null,
"cds_length": 12225,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_138694.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000371117.8"
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 67,
"exon_rank_end": null,
"exon_count": 67,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"hgvs_c": "c.12143A>G",
"hgvs_p": "p.Gln4048Arg",
"transcript": "XM_011514680.4",
"protein_id": "XP_011512982.1",
"transcript_support_level": null,
"aa_start": 4048,
"aa_end": null,
"aa_length": 4074,
"cds_start": 12143,
"cds_end": null,
"cds_length": 12225,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011514680.4"
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 67,
"exon_rank_end": null,
"exon_count": 67,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"hgvs_c": "c.12143A>G",
"hgvs_p": "p.Gln4048Arg",
"transcript": "XM_017010944.3",
"protein_id": "XP_016866433.1",
"transcript_support_level": null,
"aa_start": 4048,
"aa_end": null,
"aa_length": 4074,
"cds_start": 12143,
"cds_end": null,
"cds_length": 12225,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017010944.3"
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 66,
"exon_rank_end": null,
"exon_count": 66,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"hgvs_c": "c.12068A>G",
"hgvs_p": "p.Gln4023Arg",
"transcript": "XM_017010945.3",
"protein_id": "XP_016866434.1",
"transcript_support_level": null,
"aa_start": 4023,
"aa_end": null,
"aa_length": 4049,
"cds_start": 12068,
"cds_end": null,
"cds_length": 12150,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017010945.3"
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 66,
"exon_rank_end": null,
"exon_count": 66,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"hgvs_c": "c.12005A>G",
"hgvs_p": "p.Gln4002Arg",
"transcript": "XM_011514682.4",
"protein_id": "XP_011512984.1",
"transcript_support_level": null,
"aa_start": 4002,
"aa_end": null,
"aa_length": 4028,
"cds_start": 12005,
"cds_end": null,
"cds_length": 12087,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011514682.4"
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 65,
"exon_rank_end": null,
"exon_count": 65,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"hgvs_c": "c.11948A>G",
"hgvs_p": "p.Gln3983Arg",
"transcript": "XM_017010946.3",
"protein_id": "XP_016866435.1",
"transcript_support_level": null,
"aa_start": 3983,
"aa_end": null,
"aa_length": 4009,
"cds_start": 11948,
"cds_end": null,
"cds_length": 12030,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017010946.3"
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 65,
"exon_rank_end": null,
"exon_count": 65,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"hgvs_c": "c.11879A>G",
"hgvs_p": "p.Gln3960Arg",
"transcript": "XM_017010947.3",
"protein_id": "XP_016866436.1",
"transcript_support_level": null,
"aa_start": 3960,
"aa_end": null,
"aa_length": 3986,
"cds_start": 11879,
"cds_end": null,
"cds_length": 11961,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017010947.3"
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 68,
"exon_rank_end": null,
"exon_count": 68,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"hgvs_c": "c.11501A>G",
"hgvs_p": "p.Gln3834Arg",
"transcript": "XM_011514683.4",
"protein_id": "XP_011512985.1",
"transcript_support_level": null,
"aa_start": 3834,
"aa_end": null,
"aa_length": 3860,
"cds_start": 11501,
"cds_end": null,
"cds_length": 11583,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011514683.4"
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 59,
"exon_rank_end": null,
"exon_count": 59,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"hgvs_c": "c.11432A>G",
"hgvs_p": "p.Gln3811Arg",
"transcript": "XM_011514684.4",
"protein_id": "XP_011512986.1",
"transcript_support_level": null,
"aa_start": 3811,
"aa_end": null,
"aa_length": 3837,
"cds_start": 11432,
"cds_end": null,
"cds_length": 11514,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011514684.4"
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 58,
"exon_rank_end": null,
"exon_count": 58,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"hgvs_c": "c.11432A>G",
"hgvs_p": "p.Gln3811Arg",
"transcript": "XM_017010948.3",
"protein_id": "XP_016866437.1",
"transcript_support_level": null,
"aa_start": 3811,
"aa_end": null,
"aa_length": 3837,
"cds_start": 11432,
"cds_end": null,
"cds_length": 11514,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017010948.3"
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 49,
"exon_rank_end": null,
"exon_count": 49,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"hgvs_c": "c.10283A>G",
"hgvs_p": "p.Gln3428Arg",
"transcript": "XM_017010949.3",
"protein_id": "XP_016866438.1",
"transcript_support_level": null,
"aa_start": 3428,
"aa_end": null,
"aa_length": 3454,
"cds_start": 10283,
"cds_end": null,
"cds_length": 10365,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017010949.3"
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 32,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"hgvs_c": "c.6218A>G",
"hgvs_p": "p.Gln2073Arg",
"transcript": "XM_011514690.4",
"protein_id": "XP_011512992.1",
"transcript_support_level": null,
"aa_start": 2073,
"aa_end": null,
"aa_length": 2099,
"cds_start": 6218,
"cds_end": null,
"cds_length": 6300,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011514690.4"
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 32,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"hgvs_c": "c.6218A>G",
"hgvs_p": "p.Gln2073Arg",
"transcript": "XM_011514691.4",
"protein_id": "XP_011512993.1",
"transcript_support_level": null,
"aa_start": 2073,
"aa_end": null,
"aa_length": 2099,
"cds_start": 6218,
"cds_end": null,
"cds_length": 6300,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011514691.4"
},
{
"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": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000228689",
"gene_hgnc_id": null,
"hgvs_c": "n.81-3192T>C",
"hgvs_p": null,
"transcript": "ENST00000454361.1",
"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": "pseudogene",
"feature": "ENST00000454361.1"
},
{
"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": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ENSG00000228689",
"gene_hgnc_id": null,
"hgvs_c": "n.811-3197T>C",
"hgvs_p": null,
"transcript": "ENST00000589278.6",
"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": "ENST00000589278.6"
},
{
"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": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000228689",
"gene_hgnc_id": null,
"hgvs_c": "n.222-3192T>C",
"hgvs_p": null,
"transcript": "ENST00000650088.1",
"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": "ENST00000650088.1"
}
],
"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"dbsnp": "rs9381994",
"frequency_reference_population": 0.55403787,
"hom_count_reference_population": 248948,
"allele_count_reference_population": 894165,
"gnomad_exomes_af": 0.556297,
"gnomad_genomes_af": 0.532347,
"gnomad_exomes_ac": 813130,
"gnomad_genomes_ac": 81035,
"gnomad_exomes_homalt": 227239,
"gnomad_genomes_homalt": 21709,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.000010750293768069241,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.213,
"revel_prediction": "Benign",
"alphamissense_score": 0.0736,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.4,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.422,
"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": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BA1",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "NM_138694.4",
"gene_symbol": "PKHD1",
"hgnc_id": 9016,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.12143A>G",
"hgvs_p": "p.Gln4048Arg"
},
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000454361.1",
"gene_symbol": "ENSG00000228689",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.81-3192T>C",
"hgvs_p": null
}
],
"clinvar_disease": "Autosomal recessive polycystic kidney disease,Polycystic kidney disease,Polycystic kidney disease 4,not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:8",
"phenotype_combined": "not specified|Autosomal recessive polycystic kidney disease|Polycystic kidney disease 4|not provided|Polycystic kidney disease",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}