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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: 4-109689433-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=109689433&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 109689433,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_001226.4",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASP6",
"gene_hgnc_id": 1507,
"hgvs_c": "c.779G>A",
"hgvs_p": "p.Arg260Gln",
"transcript": "NM_001226.4",
"protein_id": "NP_001217.2",
"transcript_support_level": null,
"aa_start": 260,
"aa_end": null,
"aa_length": 293,
"cds_start": 779,
"cds_end": null,
"cds_length": 882,
"cdna_start": 829,
"cdna_end": null,
"cdna_length": 1634,
"mane_select": "ENST00000265164.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASP6",
"gene_hgnc_id": 1507,
"hgvs_c": "c.779G>A",
"hgvs_p": "p.Arg260Gln",
"transcript": "ENST00000265164.7",
"protein_id": "ENSP00000265164.2",
"transcript_support_level": 1,
"aa_start": 260,
"aa_end": null,
"aa_length": 293,
"cds_start": 779,
"cds_end": null,
"cds_length": 882,
"cdna_start": 829,
"cdna_end": null,
"cdna_length": 1634,
"mane_select": "NM_001226.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASP6",
"gene_hgnc_id": 1507,
"hgvs_c": "c.512G>A",
"hgvs_p": "p.Arg171Gln",
"transcript": "ENST00000352981.7",
"protein_id": "ENSP00000285333.3",
"transcript_support_level": 1,
"aa_start": 171,
"aa_end": null,
"aa_length": 204,
"cds_start": 512,
"cds_end": null,
"cds_length": 615,
"cdna_start": 536,
"cdna_end": null,
"cdna_length": 1347,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASP6",
"gene_hgnc_id": 1507,
"hgvs_c": "c.512G>A",
"hgvs_p": "p.Arg171Gln",
"transcript": "NM_032992.3",
"protein_id": "NP_116787.1",
"transcript_support_level": null,
"aa_start": 171,
"aa_end": null,
"aa_length": 204,
"cds_start": 512,
"cds_end": null,
"cds_length": 615,
"cdna_start": 562,
"cdna_end": null,
"cdna_length": 1367,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASP6",
"gene_hgnc_id": 1507,
"hgvs_c": "c.755G>A",
"hgvs_p": "p.Arg252Gln",
"transcript": "XM_047416244.1",
"protein_id": "XP_047272200.1",
"transcript_support_level": null,
"aa_start": 252,
"aa_end": null,
"aa_length": 285,
"cds_start": 755,
"cds_end": null,
"cds_length": 858,
"cdna_start": 2052,
"cdna_end": null,
"cdna_length": 2857,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASP6",
"gene_hgnc_id": 1507,
"hgvs_c": "n.558G>A",
"hgvs_p": null,
"transcript": "ENST00000505117.5",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 774,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASP6",
"gene_hgnc_id": 1507,
"hgvs_c": "n.*459G>A",
"hgvs_p": null,
"transcript": "ENST00000505486.2",
"protein_id": "ENSP00000424080.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1456,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASP6",
"gene_hgnc_id": 1507,
"hgvs_c": "n.361G>A",
"hgvs_p": null,
"transcript": "ENST00000507550.5",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 892,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASP6",
"gene_hgnc_id": 1507,
"hgvs_c": "n.473G>A",
"hgvs_p": null,
"transcript": "ENST00000510324.1",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 643,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASP6",
"gene_hgnc_id": 1507,
"hgvs_c": "n.752G>A",
"hgvs_p": null,
"transcript": "NR_133012.2",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1557,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASP6",
"gene_hgnc_id": 1507,
"hgvs_c": "n.*459G>A",
"hgvs_p": null,
"transcript": "ENST00000505486.2",
"protein_id": "ENSP00000424080.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1456,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "CASP6",
"gene_hgnc_id": 1507,
"hgvs_c": "c.483+5092G>A",
"hgvs_p": null,
"transcript": "XM_047416245.1",
"protein_id": "XP_047272201.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 166,
"cds_start": -4,
"cds_end": null,
"cds_length": 501,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8828,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "CASP6",
"gene_hgnc_id": 1507,
"dbsnp": "rs190973032",
"frequency_reference_population": 0.00005141885,
"hom_count_reference_population": 0,
"allele_count_reference_population": 83,
"gnomad_exomes_af": 0.0000513035,
"gnomad_genomes_af": 0.0000525258,
"gnomad_exomes_ac": 75,
"gnomad_genomes_ac": 8,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.055082082748413086,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.083,
"revel_prediction": "Benign",
"alphamissense_score": 0.1175,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.56,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.091,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -4,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Strong",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "NM_001226.4",
"gene_symbol": "CASP6",
"hgnc_id": 1507,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.779G>A",
"hgvs_p": "p.Arg260Gln"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}