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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: X-53985158-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=53985158&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 53985158,
"ref": "G",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "ENST00000338154.11",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF8",
"gene_hgnc_id": 20672,
"hgvs_c": "c.2199C>T",
"hgvs_p": "p.Ser733Ser",
"transcript": "NM_015107.3",
"protein_id": "NP_055922.1",
"transcript_support_level": null,
"aa_start": 733,
"aa_end": null,
"aa_length": 1024,
"cds_start": 2199,
"cds_end": null,
"cds_length": 3075,
"cdna_start": 3003,
"cdna_end": null,
"cdna_length": 6357,
"mane_select": "ENST00000338154.11",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF8",
"gene_hgnc_id": 20672,
"hgvs_c": "c.2199C>T",
"hgvs_p": "p.Ser733Ser",
"transcript": "ENST00000338154.11",
"protein_id": "ENSP00000338868.6",
"transcript_support_level": 1,
"aa_start": 733,
"aa_end": null,
"aa_length": 1024,
"cds_start": 2199,
"cds_end": null,
"cds_length": 3075,
"cdna_start": 3003,
"cdna_end": null,
"cdna_length": 6357,
"mane_select": "NM_015107.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF8",
"gene_hgnc_id": 20672,
"hgvs_c": "c.2307C>T",
"hgvs_p": "p.Ser769Ser",
"transcript": "ENST00000357988.9",
"protein_id": "ENSP00000350676.5",
"transcript_support_level": 1,
"aa_start": 769,
"aa_end": null,
"aa_length": 1060,
"cds_start": 2307,
"cds_end": null,
"cds_length": 3183,
"cdna_start": 2666,
"cdna_end": null,
"cdna_length": 6024,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF8",
"gene_hgnc_id": 20672,
"hgvs_c": "c.2148C>T",
"hgvs_p": "p.Ser716Ser",
"transcript": "ENST00000322659.12",
"protein_id": "ENSP00000319473.8",
"transcript_support_level": 1,
"aa_start": 716,
"aa_end": null,
"aa_length": 878,
"cds_start": 2148,
"cds_end": null,
"cds_length": 2637,
"cdna_start": 2324,
"cdna_end": null,
"cdna_length": 2921,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF8",
"gene_hgnc_id": 20672,
"hgvs_c": "c.1488C>T",
"hgvs_p": "p.Ser496Ser",
"transcript": "ENST00000443302.5",
"protein_id": "ENSP00000397129.1",
"transcript_support_level": 1,
"aa_start": 496,
"aa_end": null,
"aa_length": 658,
"cds_start": 1488,
"cds_end": null,
"cds_length": 1977,
"cdna_start": 1489,
"cdna_end": null,
"cdna_length": 2724,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF8",
"gene_hgnc_id": 20672,
"hgvs_c": "c.2307C>T",
"hgvs_p": "p.Ser769Ser",
"transcript": "NM_001184896.1",
"protein_id": "NP_001171825.1",
"transcript_support_level": null,
"aa_start": 769,
"aa_end": null,
"aa_length": 1060,
"cds_start": 2307,
"cds_end": null,
"cds_length": 3183,
"cdna_start": 2553,
"cdna_end": null,
"cdna_length": 5907,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF8",
"gene_hgnc_id": 20672,
"hgvs_c": "c.2199C>T",
"hgvs_p": "p.Ser733Ser",
"transcript": "ENST00000396282.7",
"protein_id": "ENSP00000379578.3",
"transcript_support_level": 5,
"aa_start": 733,
"aa_end": null,
"aa_length": 1049,
"cds_start": 2199,
"cds_end": null,
"cds_length": 3150,
"cdna_start": 2199,
"cdna_end": null,
"cdna_length": 3633,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF8",
"gene_hgnc_id": 20672,
"hgvs_c": "c.2004C>T",
"hgvs_p": "p.Ser668Ser",
"transcript": "NM_001441096.1",
"protein_id": "NP_001428025.1",
"transcript_support_level": null,
"aa_start": 668,
"aa_end": null,
"aa_length": 984,
"cds_start": 2004,
"cds_end": null,
"cds_length": 2955,
"cdna_start": 2250,
"cdna_end": null,
"cdna_length": 4502,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF8",
"gene_hgnc_id": 20672,
"hgvs_c": "c.1896C>T",
"hgvs_p": "p.Ser632Ser",
"transcript": "NM_001184897.2",
"protein_id": "NP_001171826.1",
"transcript_support_level": null,
"aa_start": 632,
"aa_end": null,
"aa_length": 948,
"cds_start": 1896,
"cds_end": null,
"cds_length": 2847,
"cdna_start": 2700,
"cdna_end": null,
"cdna_length": 4952,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF8",
"gene_hgnc_id": 20672,
"hgvs_c": "c.2307C>T",
"hgvs_p": "p.Ser769Ser",
"transcript": "NM_001441097.1",
"protein_id": "NP_001428026.1",
"transcript_support_level": null,
"aa_start": 769,
"aa_end": null,
"aa_length": 931,
"cds_start": 2307,
"cds_end": null,
"cds_length": 2796,
"cdna_start": 2553,
"cdna_end": null,
"cdna_length": 3791,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF8",
"gene_hgnc_id": 20672,
"hgvs_c": "c.1896C>T",
"hgvs_p": "p.Ser632Ser",
"transcript": "ENST00000338946.11",
"protein_id": "ENSP00000340051.7",
"transcript_support_level": 2,
"aa_start": 632,
"aa_end": null,
"aa_length": 923,
"cds_start": 1896,
"cds_end": null,
"cds_length": 2772,
"cdna_start": 1896,
"cdna_end": null,
"cdna_length": 5236,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF8",
"gene_hgnc_id": 20672,
"hgvs_c": "c.2148C>T",
"hgvs_p": "p.Ser716Ser",
"transcript": "NM_001184898.2",
"protein_id": "NP_001171827.1",
"transcript_support_level": null,
"aa_start": 716,
"aa_end": null,
"aa_length": 878,
"cds_start": 2148,
"cds_end": null,
"cds_length": 2637,
"cdna_start": 2277,
"cdna_end": null,
"cdna_length": 3515,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF8",
"gene_hgnc_id": 20672,
"hgvs_c": "c.2004C>T",
"hgvs_p": "p.Ser668Ser",
"transcript": "NM_001441098.1",
"protein_id": "NP_001428027.1",
"transcript_support_level": null,
"aa_start": 668,
"aa_end": null,
"aa_length": 830,
"cds_start": 2004,
"cds_end": null,
"cds_length": 2493,
"cdna_start": 2250,
"cdna_end": null,
"cdna_length": 3488,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF8",
"gene_hgnc_id": 20672,
"hgvs_c": "c.2307C>T",
"hgvs_p": "p.Ser769Ser",
"transcript": "XM_005261996.2",
"protein_id": "XP_005262053.1",
"transcript_support_level": null,
"aa_start": 769,
"aa_end": null,
"aa_length": 1085,
"cds_start": 2307,
"cds_end": null,
"cds_length": 3258,
"cdna_start": 2398,
"cdna_end": null,
"cdna_length": 4650,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF8",
"gene_hgnc_id": 20672,
"hgvs_c": "c.2307C>T",
"hgvs_p": "p.Ser769Ser",
"transcript": "XM_011530778.2",
"protein_id": "XP_011529080.1",
"transcript_support_level": null,
"aa_start": 769,
"aa_end": null,
"aa_length": 1085,
"cds_start": 2307,
"cds_end": null,
"cds_length": 3258,
"cdna_start": 2456,
"cdna_end": null,
"cdna_length": 4708,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF8",
"gene_hgnc_id": 20672,
"hgvs_c": "c.2307C>T",
"hgvs_p": "p.Ser769Ser",
"transcript": "XM_047441934.1",
"protein_id": "XP_047297890.1",
"transcript_support_level": null,
"aa_start": 769,
"aa_end": null,
"aa_length": 1060,
"cds_start": 2307,
"cds_end": null,
"cds_length": 3183,
"cdna_start": 2428,
"cdna_end": null,
"cdna_length": 5782,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF8",
"gene_hgnc_id": 20672,
"hgvs_c": "c.2199C>T",
"hgvs_p": "p.Ser733Ser",
"transcript": "XM_005261999.2",
"protein_id": "XP_005262056.1",
"transcript_support_level": null,
"aa_start": 733,
"aa_end": null,
"aa_length": 1049,
"cds_start": 2199,
"cds_end": null,
"cds_length": 3150,
"cdna_start": 3654,
"cdna_end": null,
"cdna_length": 5906,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF8",
"gene_hgnc_id": 20672,
"hgvs_c": "c.2199C>T",
"hgvs_p": "p.Ser733Ser",
"transcript": "XM_047441935.1",
"protein_id": "XP_047297891.1",
"transcript_support_level": null,
"aa_start": 733,
"aa_end": null,
"aa_length": 1049,
"cds_start": 2199,
"cds_end": null,
"cds_length": 3150,
"cdna_start": 2361,
"cdna_end": null,
"cdna_length": 4613,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF8",
"gene_hgnc_id": 20672,
"hgvs_c": "n.*654C>T",
"hgvs_p": null,
"transcript": "ENST00000686349.1",
"protein_id": "ENSP00000510424.1",
"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": 6524,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF8",
"gene_hgnc_id": 20672,
"hgvs_c": "n.*1641C>T",
"hgvs_p": null,
"transcript": "ENST00000687764.1",
"protein_id": "ENSP00000509967.1",
"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": 6476,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF8",
"gene_hgnc_id": 20672,
"hgvs_c": "n.1563C>T",
"hgvs_p": null,
"transcript": "ENST00000691629.1",
"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": 4903,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF8",
"gene_hgnc_id": 20672,
"hgvs_c": "n.*654C>T",
"hgvs_p": null,
"transcript": "ENST00000686349.1",
"protein_id": "ENSP00000510424.1",
"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": 6524,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF8",
"gene_hgnc_id": 20672,
"hgvs_c": "n.*1641C>T",
"hgvs_p": null,
"transcript": "ENST00000687764.1",
"protein_id": "ENSP00000509967.1",
"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": 6476,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PHF8",
"gene_hgnc_id": 20672,
"dbsnp": "rs201824053",
"frequency_reference_population": 0.00015686562,
"hom_count_reference_population": 69,
"allele_count_reference_population": 189,
"gnomad_exomes_af": 0.000164725,
"gnomad_genomes_af": 0.0000802711,
"gnomad_exomes_ac": 180,
"gnomad_genomes_ac": 9,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.19200000166893005,
"computational_prediction_selected": "Benign",
"computational_source_selected": "REVEL",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.192,
"revel_prediction": "Benign",
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.51,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.097,
"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": -12,
"acmg_classification": "Benign",
"acmg_criteria": "BP4,BP6_Moderate,BP7,BS1,BS2",
"acmg_by_gene": [
{
"score": -12,
"benign_score": 12,
"pathogenic_score": 0,
"criteria": [
"BP4",
"BP6_Moderate",
"BP7",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000338154.11",
"gene_symbol": "PHF8",
"hgnc_id": 20672,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "XL",
"hgvs_c": "c.2199C>T",
"hgvs_p": "p.Ser733Ser"
}
],
"clinvar_disease": "PHF8-related disorder,not specified",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "not specified|PHF8-related disorder",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}