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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-53195918-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=53195918&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 53195918,
"ref": "G",
"alt": "A",
"effect": "stop_gained,splice_region_variant",
"transcript": "ENST00000375401.8",
"consequences": [
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KDM5C",
"gene_hgnc_id": 11114,
"hgvs_c": "c.3118C>T",
"hgvs_p": "p.Gln1040*",
"transcript": "NM_004187.5",
"protein_id": "NP_004178.2",
"transcript_support_level": null,
"aa_start": 1040,
"aa_end": null,
"aa_length": 1560,
"cds_start": 3118,
"cds_end": null,
"cds_length": 4683,
"cdna_start": 3436,
"cdna_end": null,
"cdna_length": 5810,
"mane_select": "ENST00000375401.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KDM5C",
"gene_hgnc_id": 11114,
"hgvs_c": "c.3118C>T",
"hgvs_p": "p.Gln1040*",
"transcript": "ENST00000375401.8",
"protein_id": "ENSP00000364550.4",
"transcript_support_level": 1,
"aa_start": 1040,
"aa_end": null,
"aa_length": 1560,
"cds_start": 3118,
"cds_end": null,
"cds_length": 4683,
"cdna_start": 3436,
"cdna_end": null,
"cdna_length": 5810,
"mane_select": "NM_004187.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KDM5C",
"gene_hgnc_id": 11114,
"hgvs_c": "c.3115C>T",
"hgvs_p": "p.Gln1039*",
"transcript": "ENST00000404049.7",
"protein_id": "ENSP00000385394.3",
"transcript_support_level": 1,
"aa_start": 1039,
"aa_end": null,
"aa_length": 1559,
"cds_start": 3115,
"cds_end": null,
"cds_length": 4680,
"cdna_start": 3402,
"cdna_end": null,
"cdna_length": 5677,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KDM5C",
"gene_hgnc_id": 11114,
"hgvs_c": "c.3115C>T",
"hgvs_p": "p.Gln1039*",
"transcript": "NM_001282622.3",
"protein_id": "NP_001269551.1",
"transcript_support_level": null,
"aa_start": 1039,
"aa_end": null,
"aa_length": 1559,
"cds_start": 3115,
"cds_end": null,
"cds_length": 4680,
"cdna_start": 3433,
"cdna_end": null,
"cdna_length": 5807,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KDM5C",
"gene_hgnc_id": 11114,
"hgvs_c": "c.3118C>T",
"hgvs_p": "p.Gln1040*",
"transcript": "NM_001353978.3",
"protein_id": "NP_001340907.1",
"transcript_support_level": null,
"aa_start": 1040,
"aa_end": null,
"aa_length": 1557,
"cds_start": 3118,
"cds_end": null,
"cds_length": 4674,
"cdna_start": 3436,
"cdna_end": null,
"cdna_length": 5801,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KDM5C",
"gene_hgnc_id": 11114,
"hgvs_c": "c.3118C>T",
"hgvs_p": "p.Gln1040*",
"transcript": "ENST00000375379.7",
"protein_id": "ENSP00000364528.3",
"transcript_support_level": 5,
"aa_start": 1040,
"aa_end": null,
"aa_length": 1557,
"cds_start": 3118,
"cds_end": null,
"cds_length": 4674,
"cdna_start": 3651,
"cdna_end": null,
"cdna_length": 5245,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KDM5C",
"gene_hgnc_id": 11114,
"hgvs_c": "c.2995C>T",
"hgvs_p": "p.Gln999*",
"transcript": "ENST00000375383.7",
"protein_id": "ENSP00000364532.3",
"transcript_support_level": 5,
"aa_start": 999,
"aa_end": null,
"aa_length": 1516,
"cds_start": 2995,
"cds_end": null,
"cds_length": 4551,
"cdna_start": 3528,
"cdna_end": null,
"cdna_length": 5122,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KDM5C",
"gene_hgnc_id": 11114,
"hgvs_c": "c.3115C>T",
"hgvs_p": "p.Gln1039*",
"transcript": "NM_001353979.2",
"protein_id": "NP_001340908.1",
"transcript_support_level": null,
"aa_start": 1039,
"aa_end": null,
"aa_length": 1451,
"cds_start": 3115,
"cds_end": null,
"cds_length": 4356,
"cdna_start": 3433,
"cdna_end": null,
"cdna_length": 4978,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KDM5C",
"gene_hgnc_id": 11114,
"hgvs_c": "c.3118C>T",
"hgvs_p": "p.Gln1040*",
"transcript": "ENST00000691505.1",
"protein_id": "ENSP00000510354.1",
"transcript_support_level": null,
"aa_start": 1040,
"aa_end": null,
"aa_length": 1450,
"cds_start": 3118,
"cds_end": null,
"cds_length": 4353,
"cdna_start": 3422,
"cdna_end": null,
"cdna_length": 4807,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KDM5C",
"gene_hgnc_id": 11114,
"hgvs_c": "c.3118C>T",
"hgvs_p": "p.Gln1040*",
"transcript": "NM_001353981.2",
"protein_id": "NP_001340910.1",
"transcript_support_level": null,
"aa_start": 1040,
"aa_end": null,
"aa_length": 1449,
"cds_start": 3118,
"cds_end": null,
"cds_length": 4350,
"cdna_start": 3436,
"cdna_end": null,
"cdna_length": 4972,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KDM5C",
"gene_hgnc_id": 11114,
"hgvs_c": "c.3118C>T",
"hgvs_p": "p.Gln1040*",
"transcript": "ENST00000685641.2",
"protein_id": "ENSP00000509818.1",
"transcript_support_level": null,
"aa_start": 1040,
"aa_end": null,
"aa_length": 1449,
"cds_start": 3118,
"cds_end": null,
"cds_length": 4350,
"cdna_start": 3453,
"cdna_end": null,
"cdna_length": 4989,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KDM5C",
"gene_hgnc_id": 11114,
"hgvs_c": "c.3115C>T",
"hgvs_p": "p.Gln1039*",
"transcript": "NM_001353982.2",
"protein_id": "NP_001340911.1",
"transcript_support_level": null,
"aa_start": 1039,
"aa_end": null,
"aa_length": 1448,
"cds_start": 3115,
"cds_end": null,
"cds_length": 4347,
"cdna_start": 3433,
"cdna_end": null,
"cdna_length": 4969,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KDM5C",
"gene_hgnc_id": 11114,
"hgvs_c": "c.3118C>T",
"hgvs_p": "p.Gln1040*",
"transcript": "NM_001353984.2",
"protein_id": "NP_001340913.1",
"transcript_support_level": null,
"aa_start": 1040,
"aa_end": null,
"aa_length": 1444,
"cds_start": 3118,
"cds_end": null,
"cds_length": 4335,
"cdna_start": 3436,
"cdna_end": null,
"cdna_length": 4928,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KDM5C",
"gene_hgnc_id": 11114,
"hgvs_c": "c.3118C>T",
"hgvs_p": "p.Gln1040*",
"transcript": "ENST00000688699.1",
"protein_id": "ENSP00000510430.1",
"transcript_support_level": null,
"aa_start": 1040,
"aa_end": null,
"aa_length": 1444,
"cds_start": 3118,
"cds_end": null,
"cds_length": 4335,
"cdna_start": 3437,
"cdna_end": null,
"cdna_length": 5170,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KDM5C",
"gene_hgnc_id": 11114,
"hgvs_c": "c.2917C>T",
"hgvs_p": "p.Gln973*",
"transcript": "NM_001146702.2",
"protein_id": "NP_001140174.1",
"transcript_support_level": null,
"aa_start": 973,
"aa_end": null,
"aa_length": 1379,
"cds_start": 2917,
"cds_end": null,
"cds_length": 4140,
"cdna_start": 3235,
"cdna_end": null,
"cdna_length": 5044,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KDM5C",
"gene_hgnc_id": 11114,
"hgvs_c": "c.2917C>T",
"hgvs_p": "p.Gln973*",
"transcript": "ENST00000452825.7",
"protein_id": "ENSP00000445176.1",
"transcript_support_level": 5,
"aa_start": 973,
"aa_end": null,
"aa_length": 1379,
"cds_start": 2917,
"cds_end": null,
"cds_length": 4140,
"cdna_start": 3450,
"cdna_end": null,
"cdna_length": 6096,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KDM5C",
"gene_hgnc_id": 11114,
"hgvs_c": "c.2623C>T",
"hgvs_p": "p.Gln875*",
"transcript": "ENST00000693277.1",
"protein_id": "ENSP00000510522.1",
"transcript_support_level": null,
"aa_start": 875,
"aa_end": null,
"aa_length": 1288,
"cds_start": 2623,
"cds_end": null,
"cds_length": 3867,
"cdna_start": 3030,
"cdna_end": null,
"cdna_length": 4512,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KDM5C",
"gene_hgnc_id": 11114,
"hgvs_c": "n.3118C>T",
"hgvs_p": null,
"transcript": "ENST00000685423.1",
"protein_id": "ENSP00000508806.1",
"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": 4749,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KDM5C",
"gene_hgnc_id": 11114,
"hgvs_c": "n.3115C>T",
"hgvs_p": null,
"transcript": "ENST00000687695.1",
"protein_id": "ENSP00000508631.1",
"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": 5061,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KDM5C",
"gene_hgnc_id": 11114,
"hgvs_c": "n.3436C>T",
"hgvs_p": null,
"transcript": "NR_148672.2",
"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": 5063,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KDM5C",
"gene_hgnc_id": 11114,
"hgvs_c": "n.3433C>T",
"hgvs_p": null,
"transcript": "NR_148673.2",
"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": 5051,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KDM5C",
"gene_hgnc_id": 11114,
"hgvs_c": "n.3313C>T",
"hgvs_p": null,
"transcript": "NR_148674.2",
"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": 4931,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "KDM5C",
"gene_hgnc_id": 11114,
"dbsnp": "rs782246658",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.5699999928474426,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.9039999842643738,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.57,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 9.971,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.01,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.9980545003227,
"dbscsnv_ada_prediction": "Pathogenic",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 13,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP3,PP5_Moderate",
"acmg_by_gene": [
{
"score": 13,
"benign_score": 0,
"pathogenic_score": 13,
"criteria": [
"PVS1",
"PM2",
"PP3",
"PP5_Moderate"
],
"verdict": "Pathogenic",
"transcript": "ENST00000375401.8",
"gene_symbol": "KDM5C",
"hgnc_id": 11114,
"effects": [
"stop_gained",
"splice_region_variant"
],
"inheritance_mode": "XL",
"hgvs_c": "c.3118C>T",
"hgvs_p": "p.Gln1040*"
}
],
"clinvar_disease": "Syndromic X-linked intellectual disability Claes-Jensen type",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "P:1",
"phenotype_combined": "Syndromic X-linked intellectual disability Claes-Jensen type",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}