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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: 16-2104572-A-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=2104572&ref=A&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "16",
"pos": 2104572,
"ref": "A",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_001009944.3",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 46,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD1",
"gene_hgnc_id": 9008,
"hgvs_c": "c.8087T>G",
"hgvs_p": "p.Leu2696Arg",
"transcript": "NM_001009944.3",
"protein_id": "NP_001009944.3",
"transcript_support_level": null,
"aa_start": 2696,
"aa_end": null,
"aa_length": 4303,
"cds_start": 8087,
"cds_end": null,
"cds_length": 12912,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000262304.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001009944.3"
},
{
"aa_ref": "L",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 46,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD1",
"gene_hgnc_id": 9008,
"hgvs_c": "c.8087T>G",
"hgvs_p": "p.Leu2696Arg",
"transcript": "ENST00000262304.9",
"protein_id": "ENSP00000262304.4",
"transcript_support_level": 1,
"aa_start": 2696,
"aa_end": null,
"aa_length": 4303,
"cds_start": 8087,
"cds_end": null,
"cds_length": 12912,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001009944.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000262304.9"
},
{
"aa_ref": "L",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 46,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD1",
"gene_hgnc_id": 9008,
"hgvs_c": "c.8087T>G",
"hgvs_p": "p.Leu2696Arg",
"transcript": "ENST00000423118.5",
"protein_id": "ENSP00000399501.1",
"transcript_support_level": 1,
"aa_start": 2696,
"aa_end": null,
"aa_length": 4302,
"cds_start": 8087,
"cds_end": null,
"cds_length": 12909,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000423118.5"
},
{
"aa_ref": "L",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 46,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD1",
"gene_hgnc_id": 9008,
"hgvs_c": "c.8087T>G",
"hgvs_p": "p.Leu2696Arg",
"transcript": "NM_000296.4",
"protein_id": "NP_000287.4",
"transcript_support_level": null,
"aa_start": 2696,
"aa_end": null,
"aa_length": 4302,
"cds_start": 8087,
"cds_end": null,
"cds_length": 12909,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_000296.4"
},
{
"aa_ref": "L",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD1",
"gene_hgnc_id": 9008,
"hgvs_c": "c.146T>G",
"hgvs_p": "p.Leu49Arg",
"transcript": "ENST00000567946.1",
"protein_id": "ENSP00000457984.1",
"transcript_support_level": 5,
"aa_start": 49,
"aa_end": null,
"aa_length": 605,
"cds_start": 146,
"cds_end": null,
"cds_length": 1820,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000567946.1"
},
{
"aa_ref": "L",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 48,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD1",
"gene_hgnc_id": 9008,
"hgvs_c": "c.8222T>G",
"hgvs_p": "p.Leu2741Arg",
"transcript": "XM_047434208.1",
"protein_id": "XP_047290164.1",
"transcript_support_level": null,
"aa_start": 2741,
"aa_end": null,
"aa_length": 4348,
"cds_start": 8222,
"cds_end": null,
"cds_length": 13047,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047434208.1"
},
{
"aa_ref": "L",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 47,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD1",
"gene_hgnc_id": 9008,
"hgvs_c": "c.8150T>G",
"hgvs_p": "p.Leu2717Arg",
"transcript": "XM_047434209.1",
"protein_id": "XP_047290165.1",
"transcript_support_level": null,
"aa_start": 2717,
"aa_end": null,
"aa_length": 4324,
"cds_start": 8150,
"cds_end": null,
"cds_length": 12975,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047434209.1"
},
{
"aa_ref": "L",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 47,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD1",
"gene_hgnc_id": 9008,
"hgvs_c": "c.8141T>G",
"hgvs_p": "p.Leu2714Arg",
"transcript": "XM_011522528.4",
"protein_id": "XP_011520830.1",
"transcript_support_level": null,
"aa_start": 2714,
"aa_end": null,
"aa_length": 4321,
"cds_start": 8141,
"cds_end": null,
"cds_length": 12966,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011522528.4"
},
{
"aa_ref": "L",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 47,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD1",
"gene_hgnc_id": 9008,
"hgvs_c": "c.8141T>G",
"hgvs_p": "p.Leu2714Arg",
"transcript": "XM_011522529.3",
"protein_id": "XP_011520831.1",
"transcript_support_level": null,
"aa_start": 2714,
"aa_end": null,
"aa_length": 4320,
"cds_start": 8141,
"cds_end": null,
"cds_length": 12963,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011522529.3"
},
{
"aa_ref": "L",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 48,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD1",
"gene_hgnc_id": 9008,
"hgvs_c": "c.8069T>G",
"hgvs_p": "p.Leu2690Arg",
"transcript": "XM_047434210.1",
"protein_id": "XP_047290166.1",
"transcript_support_level": null,
"aa_start": 2690,
"aa_end": null,
"aa_length": 4297,
"cds_start": 8069,
"cds_end": null,
"cds_length": 12894,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047434210.1"
},
{
"aa_ref": "L",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 48,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD1",
"gene_hgnc_id": 9008,
"hgvs_c": "c.8012T>G",
"hgvs_p": "p.Leu2671Arg",
"transcript": "XM_047434211.1",
"protein_id": "XP_047290167.1",
"transcript_support_level": null,
"aa_start": 2671,
"aa_end": null,
"aa_length": 4278,
"cds_start": 8012,
"cds_end": null,
"cds_length": 12837,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047434211.1"
},
{
"aa_ref": "L",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 39,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD1",
"gene_hgnc_id": 9008,
"hgvs_c": "c.6182T>G",
"hgvs_p": "p.Leu2061Arg",
"transcript": "XM_047434212.1",
"protein_id": "XP_047290168.1",
"transcript_support_level": null,
"aa_start": 2061,
"aa_end": null,
"aa_length": 3668,
"cds_start": 6182,
"cds_end": null,
"cds_length": 11007,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047434212.1"
},
{
"aa_ref": "L",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD1",
"gene_hgnc_id": 9008,
"hgvs_c": "c.5165T>G",
"hgvs_p": "p.Leu1722Arg",
"transcript": "XM_011522537.2",
"protein_id": "XP_011520839.1",
"transcript_support_level": null,
"aa_start": 1722,
"aa_end": null,
"aa_length": 3329,
"cds_start": 5165,
"cds_end": null,
"cds_length": 9990,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011522537.2"
},
{
"aa_ref": "L",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD1",
"gene_hgnc_id": 9008,
"hgvs_c": "c.5159T>G",
"hgvs_p": "p.Leu1720Arg",
"transcript": "XM_047434213.1",
"protein_id": "XP_047290169.1",
"transcript_support_level": null,
"aa_start": 1720,
"aa_end": null,
"aa_length": 3327,
"cds_start": 5159,
"cds_end": null,
"cds_length": 9984,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047434213.1"
},
{
"aa_ref": "L",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD1",
"gene_hgnc_id": 9008,
"hgvs_c": "c.5042T>G",
"hgvs_p": "p.Leu1681Arg",
"transcript": "XM_005255370.4",
"protein_id": "XP_005255427.1",
"transcript_support_level": null,
"aa_start": 1681,
"aa_end": null,
"aa_length": 3288,
"cds_start": 5042,
"cds_end": null,
"cds_length": 9867,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005255370.4"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD1",
"gene_hgnc_id": 9008,
"hgvs_c": "n.1332T>G",
"hgvs_p": null,
"transcript": "ENST00000415938.7",
"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": "ENST00000415938.7"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD1",
"gene_hgnc_id": 9008,
"hgvs_c": "n.1812T>G",
"hgvs_p": null,
"transcript": "ENST00000483731.5",
"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": "ENST00000483731.5"
},
{
"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": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD1",
"gene_hgnc_id": 9008,
"hgvs_c": "n.2223T>G",
"hgvs_p": null,
"transcript": "ENST00000486339.6",
"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": "retained_intron",
"feature": "ENST00000486339.6"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD1",
"gene_hgnc_id": 9008,
"hgvs_c": "n.2774T>G",
"hgvs_p": null,
"transcript": "ENST00000487932.5",
"protein_id": "ENSP00000457132.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000487932.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD1",
"gene_hgnc_id": 9008,
"hgvs_c": "n.2323T>G",
"hgvs_p": null,
"transcript": "ENST00000496574.6",
"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": "retained_intron",
"feature": "ENST00000496574.6"
},
{
"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": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD1",
"gene_hgnc_id": 9008,
"hgvs_c": "n.609T>G",
"hgvs_p": null,
"transcript": "ENST00000561991.5",
"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": "ENST00000561991.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD1",
"gene_hgnc_id": 9008,
"hgvs_c": "n.1795T>G",
"hgvs_p": null,
"transcript": "ENST00000565639.6",
"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": "retained_intron",
"feature": "ENST00000565639.6"
}
],
"gene_symbol": "PKD1",
"gene_hgnc_id": 9008,
"dbsnp": "rs201238819",
"frequency_reference_population": 0.0015049065,
"hom_count_reference_population": 0,
"allele_count_reference_population": 219,
"gnomad_exomes_af": 0.000411613,
"gnomad_genomes_af": 0.00150491,
"gnomad_exomes_ac": 596,
"gnomad_genomes_ac": 219,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.007776707410812378,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.07000000029802322,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.25,
"revel_prediction": "Benign",
"alphamissense_score": 0.0426,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.48,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.659,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.07,
"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": -10,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Moderate,BS1",
"acmg_by_gene": [
{
"score": -10,
"benign_score": 10,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Moderate",
"BS1"
],
"verdict": "Benign",
"transcript": "NM_001009944.3",
"gene_symbol": "PKD1",
"hgnc_id": 9008,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.8087T>G",
"hgvs_p": "p.Leu2696Arg"
}
],
"clinvar_disease": "Polycystic kidney disease,not provided",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "Polycystic kidney disease|not provided",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}