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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: 2-218584683-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=218584683&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM2",
"PP2",
"PP3_Moderate",
"PP5_Moderate"
],
"effects": [
"missense_variant"
],
"gene_symbol": "CNOT9",
"hgnc_id": 10445,
"hgvs_c": "c.392C>T",
"hgvs_p": "p.Pro131Leu",
"inheritance_mode": "AD",
"pathogenic_score": 7,
"score": 7,
"transcript": "NM_001271634.2",
"verdict": "Likely_pathogenic"
}
],
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PP2,PP3_Moderate,PP5_Moderate",
"acmg_score": 7,
"allele_count_reference_population": 0,
"alphamissense_prediction": null,
"alphamissense_score": 0.998,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.17,
"chr": "2",
"clinvar_classification": "Likely pathogenic",
"clinvar_disease": "CNOT9-associated neurodevelopmental disorder",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LP:1",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.8755334615707397,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 299,
"aa_ref": "P",
"aa_start": 131,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3820,
"cdna_start": 508,
"cds_end": null,
"cds_length": 900,
"cds_start": 392,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "NM_005444.3",
"gene_hgnc_id": 10445,
"gene_symbol": "CNOT9",
"hgvs_c": "c.392C>T",
"hgvs_p": "p.Pro131Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000273064.11",
"protein_coding": true,
"protein_id": "NP_005435.1",
"strand": true,
"transcript": "NM_005444.3",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 299,
"aa_ref": "P",
"aa_start": 131,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 3820,
"cdna_start": 508,
"cds_end": null,
"cds_length": 900,
"cds_start": 392,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000273064.11",
"gene_hgnc_id": 10445,
"gene_symbol": "CNOT9",
"hgvs_c": "c.392C>T",
"hgvs_p": "p.Pro131Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_005444.3",
"protein_coding": true,
"protein_id": "ENSP00000273064.6",
"strand": true,
"transcript": "ENST00000273064.11",
"transcript_support_level": 1
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 258,
"aa_ref": "P",
"aa_start": 131,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1126,
"cdna_start": 472,
"cds_end": null,
"cds_length": 777,
"cds_start": 392,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000295701.9",
"gene_hgnc_id": 10445,
"gene_symbol": "CNOT9",
"hgvs_c": "c.392C>T",
"hgvs_p": "p.Pro131Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000295701.5",
"strand": true,
"transcript": "ENST00000295701.9",
"transcript_support_level": 1
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 331,
"aa_ref": "P",
"aa_start": 131,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3916,
"cdna_start": 508,
"cds_end": null,
"cds_length": 996,
"cds_start": 392,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "NM_001271634.2",
"gene_hgnc_id": 10445,
"gene_symbol": "CNOT9",
"hgvs_c": "c.392C>T",
"hgvs_p": "p.Pro131Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001258563.1",
"strand": true,
"transcript": "NM_001271634.2",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 331,
"aa_ref": "P",
"aa_start": 131,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1621,
"cdna_start": 767,
"cds_end": null,
"cds_length": 996,
"cds_start": 392,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000627282.2",
"gene_hgnc_id": 10445,
"gene_symbol": "CNOT9",
"hgvs_c": "c.392C>T",
"hgvs_p": "p.Pro131Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000486540.1",
"strand": true,
"transcript": "ENST00000627282.2",
"transcript_support_level": 2
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 330,
"aa_ref": "P",
"aa_start": 131,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1964,
"cdna_start": 508,
"cds_end": null,
"cds_length": 993,
"cds_start": 392,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000934108.1",
"gene_hgnc_id": 10445,
"gene_symbol": "CNOT9",
"hgvs_c": "c.392C>T",
"hgvs_p": "p.Pro131Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000604167.1",
"strand": true,
"transcript": "ENST00000934108.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 281,
"aa_ref": "P",
"aa_start": 131,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1677,
"cdna_start": 419,
"cds_end": null,
"cds_length": 846,
"cds_start": 392,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000934110.1",
"gene_hgnc_id": 10445,
"gene_symbol": "CNOT9",
"hgvs_c": "c.392C>T",
"hgvs_p": "p.Pro131Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000604169.1",
"strand": true,
"transcript": "ENST00000934110.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 258,
"aa_ref": "P",
"aa_start": 131,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1167,
"cdna_start": 508,
"cds_end": null,
"cds_length": 777,
"cds_start": 392,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "NM_001271635.2",
"gene_hgnc_id": 10445,
"gene_symbol": "CNOT9",
"hgvs_c": "c.392C>T",
"hgvs_p": "p.Pro131Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001258564.1",
"strand": true,
"transcript": "NM_001271635.2",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 239,
"aa_ref": "P",
"aa_start": 71,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2997,
"cdna_start": 342,
"cds_end": null,
"cds_length": 720,
"cds_start": 212,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000875549.1",
"gene_hgnc_id": 10445,
"gene_symbol": "CNOT9",
"hgvs_c": "c.212C>T",
"hgvs_p": "p.Pro71Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000545608.1",
"strand": true,
"transcript": "ENST00000875549.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 246,
"aa_ref": "P",
"aa_start": 78,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3604,
"cdna_start": 292,
"cds_end": null,
"cds_length": 741,
"cds_start": 233,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "XM_047446271.1",
"gene_hgnc_id": 10445,
"gene_symbol": "CNOT9",
"hgvs_c": "c.233C>T",
"hgvs_p": "p.Pro78Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047302227.1",
"strand": true,
"transcript": "XM_047446271.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 205,
"aa_ref": "P",
"aa_start": 78,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 952,
"cdna_start": 293,
"cds_end": null,
"cds_length": 618,
"cds_start": 233,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "XM_047446272.1",
"gene_hgnc_id": 10445,
"gene_symbol": "CNOT9",
"hgvs_c": "c.233C>T",
"hgvs_p": "p.Pro78Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047302228.1",
"strand": true,
"transcript": "XM_047446272.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 127,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1352,
"cdna_start": null,
"cds_end": null,
"cds_length": 384,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000934109.1",
"gene_hgnc_id": 10445,
"gene_symbol": "CNOT9",
"hgvs_c": "c.25-7621C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000604168.1",
"strand": true,
"transcript": "ENST00000934109.1",
"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": 3710,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 7,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NR_073390.2",
"gene_hgnc_id": 10445,
"gene_symbol": "CNOT9",
"hgvs_c": "n.436+1597C>T",
"hgvs_p": null,
"intron_rank": 3,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "NR_073390.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 581,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000432877.5",
"gene_hgnc_id": 10445,
"gene_symbol": "CNOT9",
"hgvs_c": "n.*284C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000392394.1",
"strand": true,
"transcript": "ENST00000432877.5",
"transcript_support_level": 3
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs267599211",
"effect": "missense_variant",
"frequency_reference_population": null,
"gene_hgnc_id": 10445,
"gene_symbol": "CNOT9",
"gnomad_exomes_ac": null,
"gnomad_exomes_af": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Likely pathogenic",
"phenotype_combined": "CNOT9-associated neurodevelopmental disorder",
"phylop100way_prediction": "Pathogenic",
"phylop100way_score": 7.749,
"pos": 218584683,
"ref": "C",
"revel_prediction": "Uncertain_significance",
"revel_score": 0.599,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_001271634.2"
}
]
}