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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: 4-143197871-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=143197871&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 143197871,
"ref": "G",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_032557.6",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP38",
"gene_hgnc_id": 20067,
"hgvs_c": "c.997G>C",
"hgvs_p": "p.Val333Leu",
"transcript": "NM_032557.6",
"protein_id": "NP_115946.2",
"transcript_support_level": null,
"aa_start": 333,
"aa_end": null,
"aa_length": 1042,
"cds_start": 997,
"cds_end": null,
"cds_length": 3129,
"cdna_start": 1531,
"cdna_end": null,
"cdna_length": 7081,
"mane_select": "ENST00000307017.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_032557.6"
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP38",
"gene_hgnc_id": 20067,
"hgvs_c": "c.997G>C",
"hgvs_p": "p.Val333Leu",
"transcript": "ENST00000307017.9",
"protein_id": "ENSP00000303434.4",
"transcript_support_level": 1,
"aa_start": 333,
"aa_end": null,
"aa_length": 1042,
"cds_start": 997,
"cds_end": null,
"cds_length": 3129,
"cdna_start": 1531,
"cdna_end": null,
"cdna_length": 7081,
"mane_select": "NM_032557.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000307017.9"
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP38",
"gene_hgnc_id": 20067,
"hgvs_c": "c.997G>C",
"hgvs_p": "p.Val333Leu",
"transcript": "ENST00000510377.5",
"protein_id": "ENSP00000427647.1",
"transcript_support_level": 1,
"aa_start": 333,
"aa_end": null,
"aa_length": 1004,
"cds_start": 997,
"cds_end": null,
"cds_length": 3015,
"cdna_start": 1531,
"cdna_end": null,
"cdna_length": 4135,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000510377.5"
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP38",
"gene_hgnc_id": 20067,
"hgvs_c": "c.997G>C",
"hgvs_p": "p.Val333Leu",
"transcript": "ENST00000958020.1",
"protein_id": "ENSP00000628079.1",
"transcript_support_level": null,
"aa_start": 333,
"aa_end": null,
"aa_length": 1040,
"cds_start": 997,
"cds_end": null,
"cds_length": 3123,
"cdna_start": 1496,
"cdna_end": null,
"cdna_length": 4666,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000958020.1"
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP38",
"gene_hgnc_id": 20067,
"hgvs_c": "c.997G>C",
"hgvs_p": "p.Val333Leu",
"transcript": "NM_001290325.1",
"protein_id": "NP_001277254.1",
"transcript_support_level": null,
"aa_start": 333,
"aa_end": null,
"aa_length": 1004,
"cds_start": 997,
"cds_end": null,
"cds_length": 3015,
"cdna_start": 1531,
"cdna_end": null,
"cdna_length": 4123,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001290325.1"
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP38",
"gene_hgnc_id": 20067,
"hgvs_c": "c.997G>C",
"hgvs_p": "p.Val333Leu",
"transcript": "ENST00000919754.1",
"protein_id": "ENSP00000589813.1",
"transcript_support_level": null,
"aa_start": 333,
"aa_end": null,
"aa_length": 552,
"cds_start": 997,
"cds_end": null,
"cds_length": 1659,
"cdna_start": 1475,
"cdna_end": null,
"cdna_length": 3180,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000919754.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP38",
"gene_hgnc_id": 20067,
"hgvs_c": "c.-485G>C",
"hgvs_p": null,
"transcript": "NM_001290326.1",
"protein_id": "NP_001277255.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 587,
"cds_start": null,
"cds_end": null,
"cds_length": 1764,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 7197,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001290326.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "USP38",
"gene_hgnc_id": 20067,
"hgvs_c": "c.948+2026G>C",
"hgvs_p": null,
"transcript": "NM_001410848.1",
"protein_id": "NP_001397777.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1008,
"cds_start": null,
"cds_end": null,
"cds_length": 3027,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6979,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001410848.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "USP38",
"gene_hgnc_id": 20067,
"hgvs_c": "c.948+2026G>C",
"hgvs_p": null,
"transcript": "ENST00000682469.2",
"protein_id": "ENSP00000507210.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1008,
"cds_start": null,
"cds_end": null,
"cds_length": 3027,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 7805,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000682469.2"
},
{
"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": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP38",
"gene_hgnc_id": 20067,
"hgvs_c": "n.754G>C",
"hgvs_p": null,
"transcript": "ENST00000511739.1",
"protein_id": "ENSP00000424158.1",
"transcript_support_level": 2,
"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": 6376,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000511739.1"
},
{
"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": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP38",
"gene_hgnc_id": 20067,
"hgvs_c": "n.*170G>C",
"hgvs_p": null,
"transcript": "ENST00000683224.1",
"protein_id": "ENSP00000508233.1",
"transcript_support_level": null,
"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": 4618,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000683224.1"
},
{
"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": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP38",
"gene_hgnc_id": 20067,
"hgvs_c": "n.359G>C",
"hgvs_p": null,
"transcript": "ENST00000684346.1",
"protein_id": null,
"transcript_support_level": null,
"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": 2028,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000684346.1"
},
{
"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": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP38",
"gene_hgnc_id": 20067,
"hgvs_c": "n.997G>C",
"hgvs_p": null,
"transcript": "ENST00000684586.1",
"protein_id": "ENSP00000507201.1",
"transcript_support_level": null,
"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": 4066,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000684586.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP38",
"gene_hgnc_id": 20067,
"hgvs_c": "n.*170G>C",
"hgvs_p": null,
"transcript": "ENST00000683224.1",
"protein_id": "ENSP00000508233.1",
"transcript_support_level": null,
"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": 4618,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000683224.1"
}
],
"gene_symbol": "USP38",
"gene_hgnc_id": 20067,
"dbsnp": "rs1016729920",
"frequency_reference_population": 0.000015491118,
"hom_count_reference_population": 0,
"allele_count_reference_population": 25,
"gnomad_exomes_af": 0.0000150518,
"gnomad_genomes_af": 0.0000197104,
"gnomad_exomes_ac": 22,
"gnomad_genomes_ac": 3,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.6598159074783325,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.319,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.8542,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.05,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 10.003,
"phylop100way_prediction": "Pathogenic",
"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": 2,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "NM_032557.6",
"gene_symbol": "USP38",
"hgnc_id": 20067,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.997G>C",
"hgvs_p": "p.Val333Leu"
}
],
"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
}