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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: 2-218340748-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=218340748&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 218340748,
"ref": "G",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "ENST00000273077.9",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKD",
"gene_hgnc_id": 9153,
"hgvs_c": "c.486G>A",
"hgvs_p": "p.Gly162Gly",
"transcript": "NM_015488.5",
"protein_id": "NP_056303.3",
"transcript_support_level": null,
"aa_start": 162,
"aa_end": null,
"aa_length": 385,
"cds_start": 486,
"cds_end": null,
"cds_length": 1158,
"cdna_start": 503,
"cdna_end": null,
"cdna_length": 2987,
"mane_select": "ENST00000273077.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKD",
"gene_hgnc_id": 9153,
"hgvs_c": "c.486G>A",
"hgvs_p": "p.Gly162Gly",
"transcript": "ENST00000273077.9",
"protein_id": "ENSP00000273077.4",
"transcript_support_level": 1,
"aa_start": 162,
"aa_end": null,
"aa_length": 385,
"cds_start": 486,
"cds_end": null,
"cds_length": 1158,
"cdna_start": 503,
"cdna_end": null,
"cdna_length": 2987,
"mane_select": "NM_015488.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKD",
"gene_hgnc_id": 9153,
"hgvs_c": "c.414G>A",
"hgvs_p": "p.Gly138Gly",
"transcript": "ENST00000258362.7",
"protein_id": "ENSP00000258362.3",
"transcript_support_level": 1,
"aa_start": 138,
"aa_end": null,
"aa_length": 361,
"cds_start": 414,
"cds_end": null,
"cds_length": 1086,
"cdna_start": 509,
"cdna_end": null,
"cdna_length": 2991,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKD",
"gene_hgnc_id": 9153,
"hgvs_c": "c.603G>A",
"hgvs_p": "p.Gly201Gly",
"transcript": "ENST00000685415.1",
"protein_id": "ENSP00000510415.1",
"transcript_support_level": null,
"aa_start": 201,
"aa_end": null,
"aa_length": 424,
"cds_start": 603,
"cds_end": null,
"cds_length": 1275,
"cdna_start": 625,
"cdna_end": null,
"cdna_length": 3100,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKD",
"gene_hgnc_id": 9153,
"hgvs_c": "c.486G>A",
"hgvs_p": "p.Gly162Gly",
"transcript": "ENST00000436005.3",
"protein_id": "ENSP00000414400.3",
"transcript_support_level": 5,
"aa_start": 162,
"aa_end": null,
"aa_length": 382,
"cds_start": 486,
"cds_end": null,
"cds_length": 1149,
"cdna_start": 508,
"cdna_end": null,
"cdna_length": 2974,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKD",
"gene_hgnc_id": 9153,
"hgvs_c": "c.486G>A",
"hgvs_p": "p.Gly162Gly",
"transcript": "ENST00000689816.1",
"protein_id": "ENSP00000508450.1",
"transcript_support_level": null,
"aa_start": 162,
"aa_end": null,
"aa_length": 373,
"cds_start": 486,
"cds_end": null,
"cds_length": 1122,
"cdna_start": 508,
"cdna_end": null,
"cdna_length": 2919,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKD",
"gene_hgnc_id": 9153,
"hgvs_c": "c.414G>A",
"hgvs_p": "p.Gly138Gly",
"transcript": "NM_022572.4",
"protein_id": "NP_072094.1",
"transcript_support_level": null,
"aa_start": 138,
"aa_end": null,
"aa_length": 361,
"cds_start": 414,
"cds_end": null,
"cds_length": 1086,
"cdna_start": 503,
"cdna_end": null,
"cdna_length": 2987,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKD",
"gene_hgnc_id": 9153,
"hgvs_c": "c.486G>A",
"hgvs_p": "p.Gly162Gly",
"transcript": "ENST00000688179.1",
"protein_id": "ENSP00000508635.1",
"transcript_support_level": null,
"aa_start": 162,
"aa_end": null,
"aa_length": 344,
"cds_start": 486,
"cds_end": null,
"cds_length": 1035,
"cdna_start": 508,
"cdna_end": null,
"cdna_length": 2832,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKD",
"gene_hgnc_id": 9153,
"hgvs_c": "c.486G>A",
"hgvs_p": "p.Gly162Gly",
"transcript": "ENST00000687736.1",
"protein_id": "ENSP00000509627.1",
"transcript_support_level": null,
"aa_start": 162,
"aa_end": null,
"aa_length": 325,
"cds_start": 486,
"cds_end": null,
"cds_length": 978,
"cdna_start": 486,
"cdna_end": null,
"cdna_length": 2753,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKD",
"gene_hgnc_id": 9153,
"hgvs_c": "c.486G>A",
"hgvs_p": "p.Gly162Gly",
"transcript": "XM_017003771.2",
"protein_id": "XP_016859260.1",
"transcript_support_level": null,
"aa_start": 162,
"aa_end": null,
"aa_length": 356,
"cds_start": 486,
"cds_end": null,
"cds_length": 1071,
"cdna_start": 503,
"cdna_end": null,
"cdna_length": 2900,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKD",
"gene_hgnc_id": 9153,
"hgvs_c": "c.414G>A",
"hgvs_p": "p.Gly138Gly",
"transcript": "XM_017003772.2",
"protein_id": "XP_016859261.1",
"transcript_support_level": null,
"aa_start": 138,
"aa_end": null,
"aa_length": 332,
"cds_start": 414,
"cds_end": null,
"cds_length": 999,
"cdna_start": 503,
"cdna_end": null,
"cdna_length": 2900,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKD",
"gene_hgnc_id": 9153,
"hgvs_c": "n.497G>A",
"hgvs_p": null,
"transcript": "ENST00000684905.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3719,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKD",
"gene_hgnc_id": 9153,
"hgvs_c": "n.403G>A",
"hgvs_p": null,
"transcript": "ENST00000689098.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3625,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKD",
"gene_hgnc_id": 9153,
"hgvs_c": "n.536G>A",
"hgvs_p": null,
"transcript": "ENST00000689693.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
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"cdna_length": 3758,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKD",
"gene_hgnc_id": 9153,
"hgvs_c": "n.*394G>A",
"hgvs_p": null,
"transcript": "ENST00000690891.1",
"protein_id": "ENSP00000509744.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3106,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKD",
"gene_hgnc_id": 9153,
"hgvs_c": "n.*394G>A",
"hgvs_p": null,
"transcript": "ENST00000690891.1",
"protein_id": "ENSP00000509744.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
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"cdna_start": null,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PNKD",
"gene_hgnc_id": 9153,
"hgvs_c": "c.165-786G>A",
"hgvs_p": null,
"transcript": "ENST00000692295.1",
"protein_id": "ENSP00000509392.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 265,
"cds_start": -4,
"cds_end": null,
"cds_length": 798,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2601,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PNKD",
"gene_hgnc_id": 9153,
"hgvs_c": "c.237-1233G>A",
"hgvs_p": null,
"transcript": "ENST00000691220.1",
"protein_id": "ENSP00000509580.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 258,
"cds_start": -4,
"cds_end": null,
"cds_length": 777,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2580,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "CATIP-AS2",
"gene_hgnc_id": 41079,
"hgvs_c": "n.146+10412C>T",
"hgvs_p": null,
"transcript": "ENST00000411433.2",
"protein_id": null,
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"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": "PNKD",
"gene_hgnc_id": 9153,
"hgvs_c": "n.240-4060G>A",
"hgvs_p": null,
"transcript": "ENST00000691799.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
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"cdna_start": null,
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"cdna_length": 2203,
"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"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": "PNKD",
"gene_hgnc_id": 9153,
"hgvs_c": "n.165-3707G>A",
"hgvs_p": null,
"transcript": "ENST00000693423.1",
"protein_id": "ENSP00000508705.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
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"cdna_start": null,
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"cdna_length": 2308,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "CATIP-AS2",
"gene_hgnc_id": 41079,
"hgvs_c": "n.120+10412C>T",
"hgvs_p": null,
"transcript": "NR_125777.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1183,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PNKD",
"gene_hgnc_id": 9153,
"dbsnp": "rs34014804",
"frequency_reference_population": 0.044890787,
"hom_count_reference_population": 1975,
"allele_count_reference_population": 72425,
"gnomad_exomes_af": 0.0431204,
"gnomad_genomes_af": 0.0618961,
"gnomad_exomes_ac": 63009,
"gnomad_genomes_ac": 9416,
"gnomad_exomes_homalt": 1626,
"gnomad_genomes_homalt": 349,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.8399999737739563,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.05999999865889549,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.84,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -2.488,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.06,
"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": -21,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BA1",
"acmg_by_gene": [
{
"score": -21,
"benign_score": 21,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000273077.9",
"gene_symbol": "PNKD",
"hgnc_id": 9153,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.486G>A",
"hgvs_p": "p.Gly162Gly"
},
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000411433.2",
"gene_symbol": "CATIP-AS2",
"hgnc_id": 41079,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.146+10412C>T",
"hgvs_p": null
}
],
"clinvar_disease": "Paroxysmal nonkinesigenic dyskinesia,Paroxysmal nonkinesigenic dyskinesia 1,not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:6",
"phenotype_combined": "not specified|Paroxysmal nonkinesigenic dyskinesia 1|not provided|Paroxysmal nonkinesigenic dyskinesia",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}