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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: 6-31589143-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=31589143&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 4,
"criteria": [
"PM2",
"BP4_Strong"
],
"effects": [
"missense_variant"
],
"gene_symbol": "NCR3",
"hgnc_id": 19077,
"hgvs_c": "c.530C>T",
"hgvs_p": "p.Pro177Leu",
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": -2,
"transcript": "NM_147130.3",
"verdict": "Likely_benign"
},
{
"benign_score": 4,
"criteria": [
"PM2",
"BP4_Strong"
],
"effects": [
"downstream_gene_variant"
],
"gene_symbol": "LST1",
"hgnc_id": 14189,
"hgvs_c": "c.*467G>A",
"hgvs_p": null,
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": -2,
"transcript": "NM_007161.3",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong",
"acmg_score": -2,
"allele_count_reference_population": 139,
"alphamissense_prediction": "Benign",
"alphamissense_score": 0.1526,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.69,
"chr": "6",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.0389021635055542,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 201,
"aa_ref": "P",
"aa_start": 177,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1063,
"cdna_start": 815,
"cds_end": null,
"cds_length": 606,
"cds_start": 530,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "NM_147130.3",
"gene_hgnc_id": 19077,
"gene_symbol": "NCR3",
"hgvs_c": "c.530C>T",
"hgvs_p": "p.Pro177Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000340027.10",
"protein_coding": true,
"protein_id": "NP_667341.1",
"strand": false,
"transcript": "NM_147130.3",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 201,
"aa_ref": "P",
"aa_start": 177,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 1063,
"cdna_start": 815,
"cds_end": null,
"cds_length": 606,
"cds_start": 530,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000340027.10",
"gene_hgnc_id": 19077,
"gene_symbol": "NCR3",
"hgvs_c": "c.530C>T",
"hgvs_p": "p.Pro177Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_147130.3",
"protein_coding": true,
"protein_id": "ENSP00000342156.5",
"strand": false,
"transcript": "ENST00000340027.10",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 177,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1097,
"cdna_start": null,
"cds_end": null,
"cds_length": 534,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000376073.8",
"gene_hgnc_id": 19077,
"gene_symbol": "NCR3",
"hgvs_c": "c.*51C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000365241.4",
"strand": false,
"transcript": "ENST00000376073.8",
"transcript_support_level": 1
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 201,
"aa_ref": "P",
"aa_start": 177,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1000,
"cdna_start": 770,
"cds_end": null,
"cds_length": 606,
"cds_start": 530,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000934501.1",
"gene_hgnc_id": 19077,
"gene_symbol": "NCR3",
"hgvs_c": "c.530C>T",
"hgvs_p": "p.Pro177Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000604560.1",
"strand": false,
"transcript": "ENST00000934501.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 201,
"aa_ref": "P",
"aa_start": 177,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 887,
"cdna_start": 645,
"cds_end": null,
"cds_length": 606,
"cds_start": 530,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000934502.1",
"gene_hgnc_id": 19077,
"gene_symbol": "NCR3",
"hgvs_c": "c.530C>T",
"hgvs_p": "p.Pro177Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000604561.1",
"strand": false,
"transcript": "ENST00000934502.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 201,
"aa_ref": "P",
"aa_start": 177,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 973,
"cdna_start": 725,
"cds_end": null,
"cds_length": 606,
"cds_start": 530,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "XM_006715049.4",
"gene_hgnc_id": 19077,
"gene_symbol": "NCR3",
"hgvs_c": "c.530C>T",
"hgvs_p": "p.Pro177Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_006715112.1",
"strand": false,
"transcript": "XM_006715049.4",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 176,
"aa_ref": "P",
"aa_start": 152,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 988,
"cdna_start": 740,
"cds_end": null,
"cds_length": 531,
"cds_start": 455,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "XM_011514459.3",
"gene_hgnc_id": 19077,
"gene_symbol": "NCR3",
"hgvs_c": "c.455C>T",
"hgvs_p": "p.Pro152Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011512761.1",
"strand": false,
"transcript": "XM_011514459.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 177,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1118,
"cdna_start": null,
"cds_end": null,
"cds_length": 534,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "NM_001145466.2",
"gene_hgnc_id": 19077,
"gene_symbol": "NCR3",
"hgvs_c": "c.*51C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001138938.1",
"strand": false,
"transcript": "NM_001145466.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 893,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000491161.1",
"gene_hgnc_id": 19077,
"gene_symbol": "NCR3",
"hgvs_c": "n.645C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000491161.1",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 585,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000495600.5",
"gene_hgnc_id": 19077,
"gene_symbol": "NCR3",
"hgvs_c": "n.337C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000495600.5",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 97,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 666,
"cdna_start": null,
"cds_end": null,
"cds_length": 294,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_205839.3",
"gene_hgnc_id": 14189,
"gene_symbol": "LST1",
"hgvs_c": "c.*467G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000438075.7",
"protein_coding": true,
"protein_id": "NP_995311.2",
"strand": true,
"transcript": "NM_205839.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 97,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 666,
"cdna_start": null,
"cds_end": null,
"cds_length": 294,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000438075.7",
"gene_hgnc_id": 14189,
"gene_symbol": "LST1",
"hgvs_c": "c.*467G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_205839.3",
"protein_coding": true,
"protein_id": "ENSP00000391929.3",
"strand": true,
"transcript": "ENST00000438075.7",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 190,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 875,
"cdna_start": null,
"cds_end": null,
"cds_length": 573,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000376072.7",
"gene_hgnc_id": 19077,
"gene_symbol": "NCR3",
"hgvs_c": "c.*169C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000365240.3",
"strand": true,
"transcript": "ENST00000376072.7",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 104,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 648,
"cdna_start": null,
"cds_end": null,
"cds_length": 315,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000376093.6",
"gene_hgnc_id": 14189,
"gene_symbol": "LST1",
"hgvs_c": "c.*467G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000365261.2",
"strand": true,
"transcript": "ENST00000376093.6",
"transcript_support_level": 1
},
{
"aa_alt": null,
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"aa_length": 73,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 554,
"cdna_start": null,
"cds_end": null,
"cds_length": 222,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000376086.7",
"gene_hgnc_id": 14189,
"gene_symbol": "LST1",
"hgvs_c": "c.*467G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000365254.3",
"strand": true,
"transcript": "ENST00000376086.7",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 66,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 680,
"cdna_start": null,
"cds_end": null,
"cds_length": 201,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000376089.6",
"gene_hgnc_id": 14189,
"gene_symbol": "LST1",
"hgvs_c": "c.*467G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000365257.2",
"strand": true,
"transcript": "ENST00000376089.6",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 59,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 604,
"cdna_start": null,
"cds_end": null,
"cds_length": 180,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000303757.12",
"gene_hgnc_id": 14189,
"gene_symbol": "LST1",
"hgvs_c": "c.*558G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000303649.7",
"strand": true,
"transcript": "ENST00000303757.12",
"transcript_support_level": 1
},
{
"aa_alt": null,
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"aa_ref": null,
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"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 459,
"cdna_start": null,
"cds_end": null,
"cds_length": 135,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000396101.7",
"gene_hgnc_id": 14189,
"gene_symbol": "LST1",
"hgvs_c": "c.*558G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000379408.3",
"strand": true,
"transcript": "ENST00000396101.7",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 1832,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000464526.1",
"gene_hgnc_id": 14189,
"gene_symbol": "LST1",
"hgvs_c": "n.*234G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000464526.1",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 190,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 898,
"cdna_start": null,
"cds_end": null,
"cds_length": 573,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_001145467.2",
"gene_hgnc_id": 19077,
"gene_symbol": "NCR3",
"hgvs_c": "c.*169C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001138939.1",
"strand": true,
"transcript": "NM_001145467.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 165,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 541,
"cdna_start": null,
"cds_end": null,
"cds_length": 498,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000376071.4",
"gene_hgnc_id": 19077,
"gene_symbol": "NCR3",
"hgvs_c": "c.*169C>T",
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"gnomad_exomes_ac": 134,
"gnomad_exomes_af": 0.0000916815,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 5,
"gnomad_genomes_af": 0.0000328545,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Benign",
"phylop100way_score": 0.275,
"pos": 31589143,
"ref": "G",
"revel_prediction": "Benign",
"revel_score": 0.014,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.009999999776482582,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.01,
"transcript": "NM_147130.3"
}
]
}