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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: 7-6111162-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=7&pos=6111162&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "7",
"pos": 6111162,
"ref": "C",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_032172.3",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP42",
"gene_hgnc_id": 20068,
"hgvs_c": "c.29C>A",
"hgvs_p": "p.Ser10Tyr",
"transcript": "NM_032172.3",
"protein_id": "NP_115548.1",
"transcript_support_level": null,
"aa_start": 10,
"aa_end": null,
"aa_length": 1316,
"cds_start": 29,
"cds_end": null,
"cds_length": 3951,
"cdna_start": 122,
"cdna_end": null,
"cdna_length": 5090,
"mane_select": "ENST00000306177.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "Y",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP42",
"gene_hgnc_id": 20068,
"hgvs_c": "c.29C>A",
"hgvs_p": "p.Ser10Tyr",
"transcript": "ENST00000306177.10",
"protein_id": "ENSP00000301962.5",
"transcript_support_level": 5,
"aa_start": 10,
"aa_end": null,
"aa_length": 1316,
"cds_start": 29,
"cds_end": null,
"cds_length": 3951,
"cdna_start": 122,
"cdna_end": null,
"cdna_length": 5090,
"mane_select": "NM_032172.3",
"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": 2,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP42",
"gene_hgnc_id": 20068,
"hgvs_c": "n.96C>A",
"hgvs_p": null,
"transcript": "ENST00000479544.6",
"protein_id": null,
"transcript_support_level": 1,
"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": 4286,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP42",
"gene_hgnc_id": 20068,
"hgvs_c": "c.29C>A",
"hgvs_p": "p.Ser10Tyr",
"transcript": "NM_001389650.1",
"protein_id": "NP_001376579.1",
"transcript_support_level": null,
"aa_start": 10,
"aa_end": null,
"aa_length": 1327,
"cds_start": 29,
"cds_end": null,
"cds_length": 3984,
"cdna_start": 122,
"cdna_end": null,
"cdna_length": 5046,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP42",
"gene_hgnc_id": 20068,
"hgvs_c": "c.29C>A",
"hgvs_p": "p.Ser10Tyr",
"transcript": "NM_001365764.1",
"protein_id": "NP_001352693.1",
"transcript_support_level": null,
"aa_start": 10,
"aa_end": null,
"aa_length": 1324,
"cds_start": 29,
"cds_end": null,
"cds_length": 3975,
"cdna_start": 122,
"cdna_end": null,
"cdna_length": 4312,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP42",
"gene_hgnc_id": 20068,
"hgvs_c": "c.29C>A",
"hgvs_p": "p.Ser10Tyr",
"transcript": "ENST00000465073.6",
"protein_id": "ENSP00000430568.1",
"transcript_support_level": 5,
"aa_start": 10,
"aa_end": null,
"aa_length": 474,
"cds_start": 29,
"cds_end": null,
"cds_length": 1425,
"cdna_start": 94,
"cdna_end": null,
"cdna_length": 1490,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP42",
"gene_hgnc_id": 20068,
"hgvs_c": "c.29C>A",
"hgvs_p": "p.Ser10Tyr",
"transcript": "XM_006715791.2",
"protein_id": "XP_006715854.1",
"transcript_support_level": null,
"aa_start": 10,
"aa_end": null,
"aa_length": 1327,
"cds_start": 29,
"cds_end": null,
"cds_length": 3984,
"cdna_start": 605,
"cdna_end": null,
"cdna_length": 5529,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP42",
"gene_hgnc_id": 20068,
"hgvs_c": "c.29C>A",
"hgvs_p": "p.Ser10Tyr",
"transcript": "XM_011515573.2",
"protein_id": "XP_011513875.1",
"transcript_support_level": null,
"aa_start": 10,
"aa_end": null,
"aa_length": 1327,
"cds_start": 29,
"cds_end": null,
"cds_length": 3984,
"cdna_start": 507,
"cdna_end": null,
"cdna_length": 5431,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP42",
"gene_hgnc_id": 20068,
"hgvs_c": "c.29C>A",
"hgvs_p": "p.Ser10Tyr",
"transcript": "XM_024446968.2",
"protein_id": "XP_024302736.1",
"transcript_support_level": null,
"aa_start": 10,
"aa_end": null,
"aa_length": 1327,
"cds_start": 29,
"cds_end": null,
"cds_length": 3984,
"cdna_start": 625,
"cdna_end": null,
"cdna_length": 5549,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP42",
"gene_hgnc_id": 20068,
"hgvs_c": "c.29C>A",
"hgvs_p": "p.Ser10Tyr",
"transcript": "XM_024446969.2",
"protein_id": "XP_024302737.1",
"transcript_support_level": null,
"aa_start": 10,
"aa_end": null,
"aa_length": 1327,
"cds_start": 29,
"cds_end": null,
"cds_length": 3984,
"cdna_start": 711,
"cdna_end": null,
"cdna_length": 5635,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP42",
"gene_hgnc_id": 20068,
"hgvs_c": "c.29C>A",
"hgvs_p": "p.Ser10Tyr",
"transcript": "XM_047420935.1",
"protein_id": "XP_047276891.1",
"transcript_support_level": null,
"aa_start": 10,
"aa_end": null,
"aa_length": 1327,
"cds_start": 29,
"cds_end": null,
"cds_length": 3984,
"cdna_start": 912,
"cdna_end": null,
"cdna_length": 5836,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP42",
"gene_hgnc_id": 20068,
"hgvs_c": "c.29C>A",
"hgvs_p": "p.Ser10Tyr",
"transcript": "XM_047420936.1",
"protein_id": "XP_047276892.1",
"transcript_support_level": null,
"aa_start": 10,
"aa_end": null,
"aa_length": 1327,
"cds_start": 29,
"cds_end": null,
"cds_length": 3984,
"cdna_start": 757,
"cdna_end": null,
"cdna_length": 5681,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP42",
"gene_hgnc_id": 20068,
"hgvs_c": "c.29C>A",
"hgvs_p": "p.Ser10Tyr",
"transcript": "XM_047420937.1",
"protein_id": "XP_047276893.1",
"transcript_support_level": null,
"aa_start": 10,
"aa_end": null,
"aa_length": 1327,
"cds_start": 29,
"cds_end": null,
"cds_length": 3984,
"cdna_start": 723,
"cdna_end": null,
"cdna_length": 5647,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP42",
"gene_hgnc_id": 20068,
"hgvs_c": "c.29C>A",
"hgvs_p": "p.Ser10Tyr",
"transcript": "XM_047420938.1",
"protein_id": "XP_047276894.1",
"transcript_support_level": null,
"aa_start": 10,
"aa_end": null,
"aa_length": 1327,
"cds_start": 29,
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"cdna_start": 659,
"cdna_end": null,
"cdna_length": 5583,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP42",
"gene_hgnc_id": 20068,
"hgvs_c": "c.29C>A",
"hgvs_p": "p.Ser10Tyr",
"transcript": "XM_047420939.1",
"protein_id": "XP_047276895.1",
"transcript_support_level": null,
"aa_start": 10,
"aa_end": null,
"aa_length": 1327,
"cds_start": 29,
"cds_end": null,
"cds_length": 3984,
"cdna_start": 593,
"cdna_end": null,
"cdna_length": 5517,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP42",
"gene_hgnc_id": 20068,
"hgvs_c": "c.29C>A",
"hgvs_p": "p.Ser10Tyr",
"transcript": "XM_047420940.1",
"protein_id": "XP_047276896.1",
"transcript_support_level": null,
"aa_start": 10,
"aa_end": null,
"aa_length": 1327,
"cds_start": 29,
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"cdna_start": 745,
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"cdna_length": 5669,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP42",
"gene_hgnc_id": 20068,
"hgvs_c": "c.29C>A",
"hgvs_p": "p.Ser10Tyr",
"transcript": "XM_047420941.1",
"protein_id": "XP_047276897.1",
"transcript_support_level": null,
"aa_start": 10,
"aa_end": null,
"aa_length": 1327,
"cds_start": 29,
"cds_end": null,
"cds_length": 3984,
"cdna_start": 617,
"cdna_end": null,
"cdna_length": 5541,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP42",
"gene_hgnc_id": 20068,
"hgvs_c": "c.29C>A",
"hgvs_p": "p.Ser10Tyr",
"transcript": "XM_047420942.1",
"protein_id": "XP_047276898.1",
"transcript_support_level": null,
"aa_start": 10,
"aa_end": null,
"aa_length": 1327,
"cds_start": 29,
"cds_end": null,
"cds_length": 3984,
"cdna_start": 263,
"cdna_end": null,
"cdna_length": 5187,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP42",
"gene_hgnc_id": 20068,
"hgvs_c": "c.29C>A",
"hgvs_p": "p.Ser10Tyr",
"transcript": "XM_005249883.6",
"protein_id": "XP_005249940.1",
"transcript_support_level": null,
"aa_start": 10,
"aa_end": null,
"aa_length": 737,
"cds_start": 29,
"cds_end": null,
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"cdna_start": 122,
"cdna_end": null,
"cdna_length": 3001,
"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": 2,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP42",
"gene_hgnc_id": 20068,
"hgvs_c": "n.29C>A",
"hgvs_p": null,
"transcript": "ENST00000404008.6",
"protein_id": "ENSP00000385964.2",
"transcript_support_level": 2,
"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": 1380,
"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": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP42",
"gene_hgnc_id": 20068,
"hgvs_c": "n.29C>A",
"hgvs_p": null,
"transcript": "ENST00000451154.5",
"protein_id": "ENSP00000416910.1",
"transcript_support_level": 5,
"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": 520,
"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": 2,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP42",
"gene_hgnc_id": 20068,
"hgvs_c": "n.29C>A",
"hgvs_p": null,
"transcript": "ENST00000521713.1",
"protein_id": "ENSP00000431127.1",
"transcript_support_level": 5,
"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": 5017,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "USP42",
"gene_hgnc_id": 20068,
"dbsnp": "rs1333285975",
"frequency_reference_population": 0.0000034225056,
"hom_count_reference_population": 0,
"allele_count_reference_population": 5,
"gnomad_exomes_af": 0.00000342251,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 5,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.21557354927062988,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.147,
"revel_prediction": "Benign",
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.44,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 4.658,
"phylop100way_prediction": "Uncertain_significance",
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_032172.3",
"gene_symbol": "USP42",
"hgnc_id": 20068,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.29C>A",
"hgvs_p": "p.Ser10Tyr"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}