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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: 5-177306544-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=177306544&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 177306544,
"ref": "C",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_013237.4",
"consequences": [
{
"aa_ref": "Q",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRELID1",
"gene_hgnc_id": 30255,
"hgvs_c": "c.634C>A",
"hgvs_p": "p.Gln212Lys",
"transcript": "NM_013237.4",
"protein_id": "NP_037369.1",
"transcript_support_level": null,
"aa_start": 212,
"aa_end": null,
"aa_length": 219,
"cds_start": 634,
"cds_end": null,
"cds_length": 660,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000303204.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_013237.4"
},
{
"aa_ref": "Q",
"aa_alt": "K",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRELID1",
"gene_hgnc_id": 30255,
"hgvs_c": "c.634C>A",
"hgvs_p": "p.Gln212Lys",
"transcript": "ENST00000303204.9",
"protein_id": "ENSP00000302114.4",
"transcript_support_level": 1,
"aa_start": 212,
"aa_end": null,
"aa_length": 219,
"cds_start": 634,
"cds_end": null,
"cds_length": 660,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_013237.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000303204.9"
},
{
"aa_ref": "Q",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRELID1",
"gene_hgnc_id": 30255,
"hgvs_c": "c.601C>A",
"hgvs_p": "p.Gln201Lys",
"transcript": "ENST00000503216.5",
"protein_id": "ENSP00000427097.1",
"transcript_support_level": 1,
"aa_start": 201,
"aa_end": null,
"aa_length": 208,
"cds_start": 601,
"cds_end": null,
"cds_length": 627,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000503216.5"
},
{
"aa_ref": "Q",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRELID1",
"gene_hgnc_id": 30255,
"hgvs_c": "c.646C>A",
"hgvs_p": "p.Gln216Lys",
"transcript": "ENST00000902811.1",
"protein_id": "ENSP00000572870.1",
"transcript_support_level": null,
"aa_start": 216,
"aa_end": null,
"aa_length": 223,
"cds_start": 646,
"cds_end": null,
"cds_length": 672,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000902811.1"
},
{
"aa_ref": "Q",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRELID1",
"gene_hgnc_id": 30255,
"hgvs_c": "c.601C>A",
"hgvs_p": "p.Gln201Lys",
"transcript": "NM_001271828.2",
"protein_id": "NP_001258757.1",
"transcript_support_level": null,
"aa_start": 201,
"aa_end": null,
"aa_length": 208,
"cds_start": 601,
"cds_end": null,
"cds_length": 627,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001271828.2"
},
{
"aa_ref": "S",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRELID1",
"gene_hgnc_id": 30255,
"hgvs_c": "c.537C>A",
"hgvs_p": "p.Ser179Arg",
"transcript": "ENST00000503853.1",
"protein_id": "ENSP00000426351.1",
"transcript_support_level": 2,
"aa_start": 179,
"aa_end": null,
"aa_length": 201,
"cds_start": 537,
"cds_end": null,
"cds_length": 607,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000503853.1"
},
{
"aa_ref": "Q",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRELID1",
"gene_hgnc_id": 30255,
"hgvs_c": "c.520C>A",
"hgvs_p": "p.Gln174Lys",
"transcript": "ENST00000950563.1",
"protein_id": "ENSP00000620622.1",
"transcript_support_level": null,
"aa_start": 174,
"aa_end": null,
"aa_length": 181,
"cds_start": 520,
"cds_end": null,
"cds_length": 546,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000950563.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MXD3",
"gene_hgnc_id": 14008,
"hgvs_c": "c.*575G>T",
"hgvs_p": null,
"transcript": "NM_001142935.2",
"protein_id": "NP_001136407.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 193,
"cds_start": null,
"cds_end": null,
"cds_length": 582,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001142935.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MXD3",
"gene_hgnc_id": 14008,
"hgvs_c": "c.*575G>T",
"hgvs_p": null,
"transcript": "ENST00000427908.6",
"protein_id": "ENSP00000416921.2",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 193,
"cds_start": null,
"cds_end": null,
"cds_length": 582,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000427908.6"
},
{
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRELID1",
"gene_hgnc_id": 30255,
"hgvs_c": "n.*260C>A",
"hgvs_p": null,
"transcript": "ENST00000504594.5",
"protein_id": "ENSP00000421657.1",
"transcript_support_level": 3,
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000504594.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRELID1",
"gene_hgnc_id": 30255,
"hgvs_c": "n.*260C>A",
"hgvs_p": null,
"transcript": "ENST00000504594.5",
"protein_id": "ENSP00000421657.1",
"transcript_support_level": 3,
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000504594.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "MXD3",
"gene_hgnc_id": 14008,
"hgvs_c": "n.1353+1237G>T",
"hgvs_p": null,
"transcript": "ENST00000503473.5",
"protein_id": null,
"transcript_support_level": 5,
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000503473.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "MXD3",
"gene_hgnc_id": 14008,
"hgvs_c": "n.282+1237G>T",
"hgvs_p": null,
"transcript": "ENST00000509339.1",
"protein_id": null,
"transcript_support_level": 3,
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000509339.1"
}
],
"gene_symbol": "PRELID1",
"gene_hgnc_id": 30255,
"dbsnp": "rs778485653",
"frequency_reference_population": 0.000026090327,
"hom_count_reference_population": 2,
"allele_count_reference_population": 42,
"gnomad_exomes_af": 0.000028128,
"gnomad_genomes_af": 0.00000657168,
"gnomad_exomes_ac": 41,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 2,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.022721856832504272,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.078,
"revel_prediction": "Benign",
"alphamissense_score": 0.0727,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.53,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.112,
"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": -8,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BS2",
"acmg_by_gene": [
{
"score": -8,
"benign_score": 8,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_013237.4",
"gene_symbol": "PRELID1",
"hgnc_id": 30255,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.634C>A",
"hgvs_p": "p.Gln212Lys"
},
{
"score": -8,
"benign_score": 8,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_001142935.2",
"gene_symbol": "MXD3",
"hgnc_id": 14008,
"effects": [
"3_prime_UTR_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.*575G>T",
"hgvs_p": null
}
],
"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
}