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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: 21-44330349-T-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=21&pos=44330349&ref=T&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 1,
"criteria": [
"PM2",
"PP5_Very_Strong",
"BP4"
],
"effects": [
"intron_variant"
],
"gene_symbol": "CFAP410",
"hgnc_id": 1260,
"hgvs_c": "c.1000-23A>T",
"hgvs_p": null,
"inheritance_mode": "AR,AD,SD",
"pathogenic_score": 10,
"score": 9,
"transcript": "NM_001271441.2",
"verdict": "Likely_pathogenic"
},
{
"benign_score": 1,
"criteria": [
"PM2",
"PP5_Very_Strong",
"BP4"
],
"effects": [
"upstream_gene_variant"
],
"gene_symbol": "ENSG00000241728",
"hgnc_id": null,
"hgvs_c": "n.-128A>T",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 10,
"score": 9,
"transcript": "ENST00000444409.1",
"verdict": "Likely_pathogenic"
}
],
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PP5_Very_Strong,BP4",
"acmg_score": 9,
"allele_count_reference_population": 0,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.85,
"chr": "21",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_disease": "Axial spondylometaphyseal dysplasia",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:1 LP:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.8500000238418579,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": null,
"aa_end": null,
"aa_length": 256,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2221,
"cdna_start": null,
"cds_end": null,
"cds_length": 771,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 7,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_004928.3",
"gene_hgnc_id": 1260,
"gene_symbol": "CFAP410",
"hgvs_c": "c.643-23A>T",
"hgvs_p": null,
"intron_rank": 6,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000339818.9",
"protein_coding": true,
"protein_id": "NP_004919.1",
"strand": false,
"transcript": "NM_004928.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 256,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2221,
"cdna_start": null,
"cds_end": null,
"cds_length": 771,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 7,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000339818.9",
"gene_hgnc_id": 1260,
"gene_symbol": "CFAP410",
"hgvs_c": "c.643-23A>T",
"hgvs_p": null,
"intron_rank": 6,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_004928.3",
"protein_coding": true,
"protein_id": "ENSP00000344566.4",
"strand": false,
"transcript": "ENST00000339818.9",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 375,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1634,
"cdna_start": null,
"cds_end": null,
"cds_length": 1128,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 7,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000397956.7",
"gene_hgnc_id": 1260,
"gene_symbol": "CFAP410",
"hgvs_c": "c.1000-23A>T",
"hgvs_p": null,
"intron_rank": 6,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000381047.3",
"strand": false,
"transcript": "ENST00000397956.7",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 255,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1283,
"cdna_start": null,
"cds_end": null,
"cds_length": 768,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 7,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000325223.7",
"gene_hgnc_id": 1260,
"gene_symbol": "CFAP410",
"hgvs_c": "c.640-23A>T",
"hgvs_p": null,
"intron_rank": 6,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000317302.7",
"strand": false,
"transcript": "ENST00000325223.7",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 1191,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 8,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000496321.5",
"gene_hgnc_id": 1260,
"gene_symbol": "CFAP410",
"hgvs_c": "n.756-23A>T",
"hgvs_p": null,
"intron_rank": 7,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000496321.5",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 375,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2578,
"cdna_start": null,
"cds_end": null,
"cds_length": 1128,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 7,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_001271441.2",
"gene_hgnc_id": 1260,
"gene_symbol": "CFAP410",
"hgvs_c": "c.1000-23A>T",
"hgvs_p": null,
"intron_rank": 6,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001258370.1",
"strand": false,
"transcript": "NM_001271441.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 255,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2218,
"cdna_start": null,
"cds_end": null,
"cds_length": 768,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 7,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_001271440.2",
"gene_hgnc_id": 1260,
"gene_symbol": "CFAP410",
"hgvs_c": "c.640-23A>T",
"hgvs_p": null,
"intron_rank": 6,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001258369.1",
"strand": false,
"transcript": "NM_001271440.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 214,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2138,
"cdna_start": null,
"cds_end": null,
"cds_length": 645,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 8,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_001271442.1",
"gene_hgnc_id": 1260,
"gene_symbol": "CFAP410",
"hgvs_c": "c.517-23A>T",
"hgvs_p": null,
"intron_rank": 7,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001258371.1",
"strand": false,
"transcript": "NM_001271442.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 401,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2729,
"cdna_start": null,
"cds_end": null,
"cds_length": 1206,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 6,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_047440980.1",
"gene_hgnc_id": 1260,
"gene_symbol": "CFAP410",
"hgvs_c": "c.1078-23A>T",
"hgvs_p": null,
"intron_rank": 5,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047296936.1",
"strand": false,
"transcript": "XM_047440980.1",
"transcript_support_level": null
},
{
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"aa_end": null,
"aa_length": 400,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2727,
"cdna_start": null,
"cds_end": null,
"cds_length": 1203,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 6,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_047440981.1",
"gene_hgnc_id": 1260,
"gene_symbol": "CFAP410",
"hgvs_c": "c.1075-23A>T",
"hgvs_p": null,
"intron_rank": 5,
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"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047296937.1",
"strand": false,
"transcript": "XM_047440981.1",
"transcript_support_level": null
},
{
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"aa_length": 376,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2581,
"cdna_start": null,
"cds_end": null,
"cds_length": 1131,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 7,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_047440982.1",
"gene_hgnc_id": 1260,
"gene_symbol": "CFAP410",
"hgvs_c": "c.1003-23A>T",
"hgvs_p": null,
"intron_rank": 6,
"intron_rank_end": null,
"mane_plus": null,
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"protein_coding": true,
"protein_id": "XP_047296938.1",
"strand": false,
"transcript": "XM_047440982.1",
"transcript_support_level": null
},
{
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"aa_ref": null,
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"biotype": "protein_coding",
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"cdna_length": 2364,
"cdna_start": null,
"cds_end": null,
"cds_length": 846,
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"consequences": [
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],
"exon_count": 6,
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"feature": "XM_006724051.4",
"gene_hgnc_id": 1260,
"gene_symbol": "CFAP410",
"hgvs_c": "c.718-23A>T",
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"mane_plus": null,
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"protein_id": "XP_006724114.1",
"strand": false,
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},
{
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"consequences": [
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],
"exon_count": 6,
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"feature": "XM_047440983.1",
"gene_hgnc_id": 1260,
"gene_symbol": "CFAP410",
"hgvs_c": "c.715-23A>T",
"hgvs_p": null,
"intron_rank": 5,
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"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047296939.1",
"strand": false,
"transcript": "XM_047440983.1",
"transcript_support_level": null
},
{
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"aa_ref": null,
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"biotype": "protein_coding",
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"cdna_start": null,
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"consequences": [
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],
"exon_count": 6,
"exon_rank": null,
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"feature": "XM_047440984.1",
"gene_hgnc_id": 1260,
"gene_symbol": "CFAP410",
"hgvs_c": "c.679-23A>T",
"hgvs_p": null,
"intron_rank": 5,
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"mane_plus": null,
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"protein_coding": true,
"protein_id": "XP_047296940.1",
"strand": false,
"transcript": "XM_047440984.1",
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},
{
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"cds_start": null,
"consequences": [
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],
"exon_count": 5,
"exon_rank": null,
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"feature": "XM_047440985.1",
"gene_hgnc_id": 1260,
"gene_symbol": "CFAP410",
"hgvs_c": "c.679-23A>T",
"hgvs_p": null,
"intron_rank": 4,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047296941.1",
"strand": false,
"transcript": "XM_047440985.1",
"transcript_support_level": null
},
{
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"biotype": "protein_coding",
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"cdna_end": null,
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"cdna_start": null,
"cds_end": null,
"cds_length": 807,
"cds_start": null,
"consequences": [
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],
"exon_count": 6,
"exon_rank": null,
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"feature": "XM_047440986.1",
"gene_hgnc_id": 1260,
"gene_symbol": "CFAP410",
"hgvs_c": "c.679-23A>T",
"hgvs_p": null,
"intron_rank": 5,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047296942.1",
"strand": false,
"transcript": "XM_047440986.1",
"transcript_support_level": null
},
{
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"consequences": [
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],
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"feature": "XM_047440987.1",
"gene_hgnc_id": 1260,
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"hgvs_c": "c.676-23A>T",
"hgvs_p": null,
"intron_rank": 5,
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"mane_plus": null,
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"protein_coding": true,
"protein_id": "XP_047296943.1",
"strand": false,
"transcript": "XM_047440987.1",
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},
{
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"consequences": [
"intron_variant"
],
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"feature": "ENST00000462742.1",
"gene_hgnc_id": 1260,
"gene_symbol": "CFAP410",
"hgvs_c": "n.4097-23A>T",
"hgvs_p": null,
"intron_rank": 5,
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"mane_plus": null,
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"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000462742.1",
"transcript_support_level": 2
},
{
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"biotype": "pseudogene",
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"consequences": [
"intron_variant"
],
"exon_count": 3,
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"feature": "ENST00000470196.5",
"gene_hgnc_id": 1260,
"gene_symbol": "CFAP410",
"hgvs_c": "n.219-23A>T",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000470196.5",
"transcript_support_level": 2
},
{
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"aa_length": null,
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"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 619,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000444409.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000241728",
"hgvs_c": "n.-128A>T",
"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": "ENST00000444409.1",
"transcript_support_level": 2
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs1131690800",
"effect": "intron_variant",
"frequency_reference_population": null,
"gene_hgnc_id": 1260,
"gene_symbol": "CFAP410",
"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": "Pathogenic/Likely pathogenic",
"phenotype_combined": "Axial spondylometaphyseal dysplasia",
"phylop100way_prediction": "Benign",
"phylop100way_score": 0.127,
"pos": 44330349,
"ref": "T",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.10999999940395355,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.11,
"transcript": "NM_001271441.2"
}
]
}