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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: 7-66633380-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=7&pos=66633380&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM2",
"PM5",
"PP3_Moderate",
"PP5"
],
"effects": [
"missense_variant"
],
"gene_symbol": "KCTD7",
"hgnc_id": 21957,
"hgvs_c": "c.250C>T",
"hgvs_p": "p.Arg84Trp",
"inheritance_mode": "AR",
"pathogenic_score": 7,
"score": 7,
"transcript": "NM_153033.5",
"verdict": "Likely_pathogenic"
},
{
"benign_score": 0,
"criteria": [
"PM2",
"PP3_Moderate",
"PP5"
],
"effects": [
"intron_variant"
],
"gene_symbol": "ENSG00000284461",
"hgnc_id": null,
"hgvs_c": "n.144+4172C>T",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 5,
"score": 5,
"transcript": "ENST00000503687.2",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PM5,PP3_Moderate,PP5",
"acmg_score": 7,
"allele_count_reference_population": 8,
"alphamissense_prediction": null,
"alphamissense_score": 0.7963,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.31,
"chr": "7",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_disease": "Progressive myoclonic epilepsy type 3,not specified",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "LP:1 US:2",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.9121456742286682,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 289,
"aa_ref": "R",
"aa_start": 84,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4869,
"cdna_start": 434,
"cds_end": null,
"cds_length": 870,
"cds_start": 250,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "NM_153033.5",
"gene_hgnc_id": 21957,
"gene_symbol": "KCTD7",
"hgvs_c": "c.250C>T",
"hgvs_p": "p.Arg84Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000639828.2",
"protein_coding": true,
"protein_id": "NP_694578.1",
"strand": true,
"transcript": "NM_153033.5",
"transcript_support_level": null
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 289,
"aa_ref": "R",
"aa_start": 84,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 4869,
"cdna_start": 434,
"cds_end": null,
"cds_length": 870,
"cds_start": 250,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000639828.2",
"gene_hgnc_id": 21957,
"gene_symbol": "KCTD7",
"hgvs_c": "c.250C>T",
"hgvs_p": "p.Arg84Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_153033.5",
"protein_coding": true,
"protein_id": "ENSP00000492240.1",
"strand": true,
"transcript": "ENST00000639828.2",
"transcript_support_level": 2
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 288,
"aa_ref": "R",
"aa_start": 84,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1160,
"cdna_start": 372,
"cds_end": null,
"cds_length": 867,
"cds_start": 250,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000443322.1",
"gene_hgnc_id": 21957,
"gene_symbol": "KCTD7",
"hgvs_c": "c.250C>T",
"hgvs_p": "p.Arg84Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000411624.1",
"strand": true,
"transcript": "ENST00000443322.1",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": true,
"cdna_end": null,
"cdna_length": 4139,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 13,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000503687.2",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000284461",
"hgvs_c": "n.144+4172C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000421074.1",
"strand": true,
"transcript": "ENST00000503687.2",
"transcript_support_level": 2
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 304,
"aa_ref": "R",
"aa_start": 84,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4118,
"cdna_start": 430,
"cds_end": null,
"cds_length": 915,
"cds_start": 250,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000640385.1",
"gene_hgnc_id": 21957,
"gene_symbol": "KCTD7",
"hgvs_c": "c.250C>T",
"hgvs_p": "p.Arg84Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000491193.1",
"strand": true,
"transcript": "ENST00000640385.1",
"transcript_support_level": 5
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 288,
"aa_ref": "R",
"aa_start": 84,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3886,
"cdna_start": 434,
"cds_end": null,
"cds_length": 867,
"cds_start": 250,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "NM_001167961.2",
"gene_hgnc_id": 21957,
"gene_symbol": "KCTD7",
"hgvs_c": "c.250C>T",
"hgvs_p": "p.Arg84Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001161433.1",
"strand": true,
"transcript": "NM_001167961.2",
"transcript_support_level": null
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 258,
"aa_ref": "R",
"aa_start": 84,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4795,
"cdna_start": 430,
"cds_end": null,
"cds_length": 777,
"cds_start": 250,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000275532.8",
"gene_hgnc_id": 21957,
"gene_symbol": "KCTD7",
"hgvs_c": "c.250C>T",
"hgvs_p": "p.Arg84Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000275532.4",
"strand": true,
"transcript": "ENST00000275532.8",
"transcript_support_level": 4
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 238,
"aa_ref": "R",
"aa_start": 84,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3745,
"cdna_start": 261,
"cds_end": null,
"cds_length": 717,
"cds_start": 250,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000640851.1",
"gene_hgnc_id": 21957,
"gene_symbol": "KCTD7",
"hgvs_c": "c.250C>T",
"hgvs_p": "p.Arg84Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000492577.1",
"strand": true,
"transcript": "ENST00000640851.1",
"transcript_support_level": 5
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 204,
"aa_ref": "R",
"aa_start": 40,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1704,
"cdna_start": 120,
"cds_end": null,
"cds_length": 615,
"cds_start": 118,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000640234.1",
"gene_hgnc_id": 21957,
"gene_symbol": "KCTD7",
"hgvs_c": "c.118C>T",
"hgvs_p": "p.Arg40Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000491794.1",
"strand": true,
"transcript": "ENST00000640234.1",
"transcript_support_level": 5
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 186,
"aa_ref": "R",
"aa_start": 84,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5098,
"cdna_start": 262,
"cds_end": null,
"cds_length": 561,
"cds_start": 250,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000639879.1",
"gene_hgnc_id": 21957,
"gene_symbol": "KCTD7",
"hgvs_c": "c.250C>T",
"hgvs_p": "p.Arg84Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000492161.1",
"strand": true,
"transcript": "ENST00000639879.1",
"transcript_support_level": 4
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 177,
"aa_ref": "R",
"aa_start": 76,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 538,
"cdna_start": 228,
"cds_end": null,
"cds_length": 536,
"cds_start": 226,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000449064.6",
"gene_hgnc_id": 21957,
"gene_symbol": "KCTD7",
"hgvs_c": "c.226C>T",
"hgvs_p": "p.Arg76Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000388463.2",
"strand": true,
"transcript": "ENST00000449064.6",
"transcript_support_level": 4
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 136,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4471,
"cdna_start": null,
"cds_end": null,
"cds_length": 411,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000638540.1",
"gene_hgnc_id": 21957,
"gene_symbol": "KCTD7",
"hgvs_c": "c.117+4172C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000492064.1",
"strand": true,
"transcript": "ENST00000638540.1",
"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": 3747,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000638524.1",
"gene_hgnc_id": 21957,
"gene_symbol": "KCTD7",
"hgvs_c": "n.138+4172C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000491791.1",
"strand": true,
"transcript": "ENST00000638524.1",
"transcript_support_level": 5
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs754476100",
"effect": "missense_variant",
"frequency_reference_population": 0.0000054726897,
"gene_hgnc_id": 21957,
"gene_symbol": "KCTD7",
"gnomad_exomes_ac": 8,
"gnomad_exomes_af": 0.00000547269,
"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": "Conflicting classifications of pathogenicity",
"phenotype_combined": "Progressive myoclonic epilepsy type 3|not specified",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 4.519,
"pos": 66633380,
"ref": "C",
"revel_prediction": "Pathogenic",
"revel_score": 0.851,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_153033.5"
}
]
}