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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: 5-98856390-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=98856390&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 98856390,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000614616.5",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 36,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHD1",
"gene_hgnc_id": 1915,
"hgvs_c": "c.5123G>A",
"hgvs_p": "p.Arg1708Gln",
"transcript": "NM_001270.4",
"protein_id": "NP_001261.2",
"transcript_support_level": null,
"aa_start": 1708,
"aa_end": null,
"aa_length": 1710,
"cds_start": 5123,
"cds_end": null,
"cds_length": 5133,
"cdna_start": 5740,
"cdna_end": null,
"cdna_length": 8145,
"mane_select": "ENST00000614616.5",
"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": 36,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHD1",
"gene_hgnc_id": 1915,
"hgvs_c": "c.5123G>A",
"hgvs_p": "p.Arg1708Gln",
"transcript": "ENST00000614616.5",
"protein_id": "ENSP00000483667.1",
"transcript_support_level": 5,
"aa_start": 1708,
"aa_end": null,
"aa_length": 1710,
"cds_start": 5123,
"cds_end": null,
"cds_length": 5133,
"cdna_start": 5740,
"cdna_end": null,
"cdna_length": 8145,
"mane_select": "NM_001270.4",
"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": 37,
"exon_rank_end": null,
"exon_count": 37,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHD1",
"gene_hgnc_id": 1915,
"hgvs_c": "c.5387G>A",
"hgvs_p": "p.Arg1796Gln",
"transcript": "NM_001364113.3",
"protein_id": "NP_001351042.1",
"transcript_support_level": null,
"aa_start": 1796,
"aa_end": null,
"aa_length": 1798,
"cds_start": 5387,
"cds_end": null,
"cds_length": 5397,
"cdna_start": 6004,
"cdna_end": null,
"cdna_length": 8409,
"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": 37,
"exon_rank_end": null,
"exon_count": 37,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHD1",
"gene_hgnc_id": 1915,
"hgvs_c": "c.5387G>A",
"hgvs_p": "p.Arg1796Gln",
"transcript": "ENST00000511067.3",
"protein_id": "ENSP00000479403.2",
"transcript_support_level": 5,
"aa_start": 1796,
"aa_end": null,
"aa_length": 1798,
"cds_start": 5387,
"cds_end": null,
"cds_length": 5397,
"cdna_start": 6004,
"cdna_end": null,
"cdna_length": 8409,
"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": 36,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHD1",
"gene_hgnc_id": 1915,
"hgvs_c": "c.5123G>A",
"hgvs_p": "p.Arg1708Gln",
"transcript": "NM_001376194.2",
"protein_id": "NP_001363123.1",
"transcript_support_level": null,
"aa_start": 1708,
"aa_end": null,
"aa_length": 1710,
"cds_start": 5123,
"cds_end": null,
"cds_length": 5133,
"cdna_start": 5511,
"cdna_end": null,
"cdna_length": 7916,
"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": 37,
"exon_rank_end": null,
"exon_count": 37,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHD1",
"gene_hgnc_id": 1915,
"hgvs_c": "c.5387G>A",
"hgvs_p": "p.Arg1796Gln",
"transcript": "XM_024454344.2",
"protein_id": "XP_024310112.1",
"transcript_support_level": null,
"aa_start": 1796,
"aa_end": null,
"aa_length": 1798,
"cds_start": 5387,
"cds_end": null,
"cds_length": 5397,
"cdna_start": 5827,
"cdna_end": null,
"cdna_length": 8232,
"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": 36,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHD1",
"gene_hgnc_id": 1915,
"hgvs_c": "c.5123G>A",
"hgvs_p": "p.Arg1708Gln",
"transcript": "XM_047416669.1",
"protein_id": "XP_047272625.1",
"transcript_support_level": null,
"aa_start": 1708,
"aa_end": null,
"aa_length": 1710,
"cds_start": 5123,
"cds_end": null,
"cds_length": 5133,
"cdna_start": 5455,
"cdna_end": null,
"cdna_length": 7860,
"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": "CHD1",
"gene_hgnc_id": 1915,
"hgvs_c": "n.1310G>A",
"hgvs_p": null,
"transcript": "ENST00000512392.5",
"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": 1968,
"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": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHD1",
"gene_hgnc_id": 1915,
"hgvs_c": "n.*672G>A",
"hgvs_p": null,
"transcript": "ENST00000512844.5",
"protein_id": "ENSP00000422589.1",
"transcript_support_level": 5,
"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": 848,
"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": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHD1",
"gene_hgnc_id": 1915,
"hgvs_c": "n.1769G>A",
"hgvs_p": null,
"transcript": "ENST00000514344.5",
"protein_id": null,
"transcript_support_level": 5,
"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": 2955,
"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": 34,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHD1",
"gene_hgnc_id": 1915,
"hgvs_c": "n.5843G>A",
"hgvs_p": null,
"transcript": "ENST00000706140.1",
"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": 6992,
"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": 37,
"exon_rank_end": null,
"exon_count": 37,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHD1",
"gene_hgnc_id": 1915,
"hgvs_c": "n.*2651G>A",
"hgvs_p": null,
"transcript": "ENST00000706141.1",
"protein_id": "ENSP00000516225.1",
"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": 5919,
"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": 37,
"exon_rank_end": null,
"exon_count": 37,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHD1",
"gene_hgnc_id": 1915,
"hgvs_c": "n.5770G>A",
"hgvs_p": null,
"transcript": "NR_157078.3",
"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": 8175,
"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": 35,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHD1",
"gene_hgnc_id": 1915,
"hgvs_c": "n.5561G>A",
"hgvs_p": null,
"transcript": "NR_157079.3",
"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": 7966,
"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": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHD1",
"gene_hgnc_id": 1915,
"hgvs_c": "n.*672G>A",
"hgvs_p": null,
"transcript": "ENST00000512844.5",
"protein_id": "ENSP00000422589.1",
"transcript_support_level": 5,
"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": 848,
"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": 37,
"exon_rank_end": null,
"exon_count": 37,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHD1",
"gene_hgnc_id": 1915,
"hgvs_c": "n.*2651G>A",
"hgvs_p": null,
"transcript": "ENST00000706141.1",
"protein_id": "ENSP00000516225.1",
"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": 5919,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 36,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHD1",
"gene_hgnc_id": 1915,
"hgvs_c": "c.*253G>A",
"hgvs_p": null,
"transcript": "XM_024454345.2",
"protein_id": "XP_024310113.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1640,
"cds_start": -4,
"cds_end": null,
"cds_length": 4923,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8198,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 35,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHD1",
"gene_hgnc_id": 1915,
"hgvs_c": "c.*253G>A",
"hgvs_p": null,
"transcript": "XM_047416670.1",
"protein_id": "XP_047272626.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1552,
"cds_start": -4,
"cds_end": null,
"cds_length": 4659,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 7934,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000295348",
"gene_hgnc_id": null,
"hgvs_c": "n.45-12C>T",
"hgvs_p": null,
"transcript": "ENST00000729415.1",
"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": 553,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHD1",
"gene_hgnc_id": 1915,
"hgvs_c": "n.*571G>A",
"hgvs_p": null,
"transcript": "ENST00000505657.1",
"protein_id": "ENSP00000422225.1",
"transcript_support_level": 3,
"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": 736,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHD1",
"gene_hgnc_id": 1915,
"hgvs_c": "n.*35G>A",
"hgvs_p": null,
"transcript": "ENST00000513064.1",
"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": 786,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "CHD1",
"gene_hgnc_id": 1915,
"dbsnp": "rs1293161341",
"frequency_reference_population": 0.000004125458,
"hom_count_reference_population": 0,
"allele_count_reference_population": 6,
"gnomad_exomes_af": 0.00000412546,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 6,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.6453120112419128,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.639,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.4671,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.09,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 7.098,
"phylop100way_prediction": "Uncertain_significance",
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 0,
"pathogenic_score": 0,
"criteria": [],
"verdict": "Uncertain_significance",
"transcript": "ENST00000614616.5",
"gene_symbol": "CHD1",
"hgnc_id": 1915,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,Unknown,AR",
"hgvs_c": "c.5123G>A",
"hgvs_p": "p.Arg1708Gln"
},
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000729415.1",
"gene_symbol": "ENSG00000295348",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.45-12C>T",
"hgvs_p": null
}
],
"clinvar_disease": "Pilarowski-Bjornsson syndrome,not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Pilarowski-Bjornsson syndrome|not provided",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}