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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: 2-232531600-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=232531600&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM2",
"PP3_Moderate"
],
"effects": [
"missense_variant"
],
"gene_symbol": "CHRND",
"hgnc_id": 1965,
"hgvs_c": "c.991C>T",
"hgvs_p": "p.Leu331Phe",
"inheritance_mode": "AR,AD",
"pathogenic_score": 4,
"score": 4,
"transcript": "NM_000751.3",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3_Moderate",
"acmg_score": 4,
"allele_count_reference_population": 2,
"alphamissense_prediction": null,
"alphamissense_score": 0.719,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.48,
"chr": "2",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "Lethal multiple pterygium syndrome",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.9103398323059082,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 517,
"aa_ref": "L",
"aa_start": 331,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2962,
"cdna_start": 1047,
"cds_end": null,
"cds_length": 1554,
"cds_start": 991,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "NM_000751.3",
"gene_hgnc_id": 1965,
"gene_symbol": "CHRND",
"hgvs_c": "c.991C>T",
"hgvs_p": "p.Leu331Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000258385.8",
"protein_coding": true,
"protein_id": "NP_000742.1",
"strand": true,
"transcript": "NM_000751.3",
"transcript_support_level": null
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 517,
"aa_ref": "L",
"aa_start": 331,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2962,
"cdna_start": 1047,
"cds_end": null,
"cds_length": 1554,
"cds_start": 991,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000258385.8",
"gene_hgnc_id": 1965,
"gene_symbol": "CHRND",
"hgvs_c": "c.991C>T",
"hgvs_p": "p.Leu331Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_000751.3",
"protein_coding": true,
"protein_id": "ENSP00000258385.3",
"strand": true,
"transcript": "ENST00000258385.8",
"transcript_support_level": 1
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 502,
"aa_ref": "L",
"aa_start": 316,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2917,
"cdna_start": 1002,
"cds_end": null,
"cds_length": 1509,
"cds_start": 946,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "NM_001256657.2",
"gene_hgnc_id": 1965,
"gene_symbol": "CHRND",
"hgvs_c": "c.946C>T",
"hgvs_p": "p.Leu316Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001243586.1",
"strand": true,
"transcript": "NM_001256657.2",
"transcript_support_level": null
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 502,
"aa_ref": "L",
"aa_start": 316,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2918,
"cdna_start": 1002,
"cds_end": null,
"cds_length": 1509,
"cds_start": 946,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000543200.5",
"gene_hgnc_id": 1965,
"gene_symbol": "CHRND",
"hgvs_c": "c.946C>T",
"hgvs_p": "p.Leu316Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000438380.1",
"strand": true,
"transcript": "ENST00000543200.5",
"transcript_support_level": 2
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 450,
"aa_ref": "L",
"aa_start": 264,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2764,
"cdna_start": 846,
"cds_end": null,
"cds_length": 1353,
"cds_start": 790,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000955151.1",
"gene_hgnc_id": 1965,
"gene_symbol": "CHRND",
"hgvs_c": "c.790C>T",
"hgvs_p": "p.Leu264Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000625210.1",
"strand": true,
"transcript": "ENST00000955151.1",
"transcript_support_level": null
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 416,
"aa_ref": "L",
"aa_start": 230,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2930,
"cdna_start": 1015,
"cds_end": null,
"cds_length": 1251,
"cds_start": 688,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "NM_001311196.2",
"gene_hgnc_id": 1965,
"gene_symbol": "CHRND",
"hgvs_c": "c.688C>T",
"hgvs_p": "p.Leu230Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001298125.1",
"strand": true,
"transcript": "NM_001311196.2",
"transcript_support_level": null
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 323,
"aa_ref": "L",
"aa_start": 137,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2651,
"cdna_start": 736,
"cds_end": null,
"cds_length": 972,
"cds_start": 409,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "NM_001311195.2",
"gene_hgnc_id": 1965,
"gene_symbol": "CHRND",
"hgvs_c": "c.409C>T",
"hgvs_p": "p.Leu137Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001298124.1",
"strand": true,
"transcript": "NM_001311195.2",
"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": 735,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000412233.5",
"gene_hgnc_id": 1965,
"gene_symbol": "CHRND",
"hgvs_c": "n.*164C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000398143.1",
"strand": true,
"transcript": "ENST00000412233.5",
"transcript_support_level": 4
},
{
"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": 3022,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 11,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000441621.6",
"gene_hgnc_id": 1965,
"gene_symbol": "CHRND",
"hgvs_c": "n.*173C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000408819.2",
"strand": true,
"transcript": "ENST00000441621.6",
"transcript_support_level": 5
},
{
"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": 1580,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 12,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000446616.1",
"gene_hgnc_id": 1965,
"gene_symbol": "CHRND",
"hgvs_c": "n.*632C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000410801.1",
"strand": true,
"transcript": "ENST00000446616.1",
"transcript_support_level": 3
},
{
"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": 735,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000412233.5",
"gene_hgnc_id": 1965,
"gene_symbol": "CHRND",
"hgvs_c": "n.*164C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000398143.1",
"strand": true,
"transcript": "ENST00000412233.5",
"transcript_support_level": 4
},
{
"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": 3022,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 11,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000441621.6",
"gene_hgnc_id": 1965,
"gene_symbol": "CHRND",
"hgvs_c": "n.*173C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000408819.2",
"strand": true,
"transcript": "ENST00000441621.6",
"transcript_support_level": 5
},
{
"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": 1580,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 12,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000446616.1",
"gene_hgnc_id": 1965,
"gene_symbol": "CHRND",
"hgvs_c": "n.*632C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000410801.1",
"strand": true,
"transcript": "ENST00000446616.1",
"transcript_support_level": 3
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs1292476417",
"effect": "missense_variant",
"frequency_reference_population": 0.0000013682323,
"gene_hgnc_id": 1965,
"gene_symbol": "CHRND",
"gnomad_exomes_ac": 2,
"gnomad_exomes_af": 0.00000136823,
"gnomad_exomes_homalt": 0,
"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": "Uncertain significance",
"phenotype_combined": "Lethal multiple pterygium syndrome",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 4.987,
"pos": 232531600,
"ref": "C",
"revel_prediction": "Pathogenic",
"revel_score": 0.766,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_000751.3"
}
]
}