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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: 4-110618669-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=110618669&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 110618669,
"ref": "C",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000644743.1",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PITX2",
"gene_hgnc_id": 9005,
"hgvs_c": "c.431G>C",
"hgvs_p": "p.Arg144Pro",
"transcript": "NM_000325.6",
"protein_id": "NP_000316.2",
"transcript_support_level": null,
"aa_start": 144,
"aa_end": null,
"aa_length": 324,
"cds_start": 431,
"cds_end": null,
"cds_length": 975,
"cdna_start": 1048,
"cdna_end": null,
"cdna_length": 2294,
"mane_select": "ENST00000644743.1",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "P",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PITX2",
"gene_hgnc_id": 9005,
"hgvs_c": "c.431G>C",
"hgvs_p": "p.Arg144Pro",
"transcript": "ENST00000644743.1",
"protein_id": "ENSP00000495061.1",
"transcript_support_level": null,
"aa_start": 144,
"aa_end": null,
"aa_length": 324,
"cds_start": 431,
"cds_end": null,
"cds_length": 975,
"cdna_start": 1048,
"cdna_end": null,
"cdna_length": 2294,
"mane_select": "NM_000325.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "P",
"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": "PITX2",
"gene_hgnc_id": 9005,
"hgvs_c": "c.272G>C",
"hgvs_p": "p.Arg91Pro",
"transcript": "ENST00000355080.9",
"protein_id": "ENSP00000347192.5",
"transcript_support_level": 1,
"aa_start": 91,
"aa_end": null,
"aa_length": 271,
"cds_start": 272,
"cds_end": null,
"cds_length": 816,
"cdna_start": 854,
"cdna_end": null,
"cdna_length": 2100,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PITX2",
"gene_hgnc_id": 9005,
"hgvs_c": "c.410G>C",
"hgvs_p": "p.Arg137Pro",
"transcript": "NM_001204397.2",
"protein_id": "NP_001191326.1",
"transcript_support_level": null,
"aa_start": 137,
"aa_end": null,
"aa_length": 317,
"cds_start": 410,
"cds_end": null,
"cds_length": 954,
"cdna_start": 885,
"cdna_end": null,
"cdna_length": 2131,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PITX2",
"gene_hgnc_id": 9005,
"hgvs_c": "c.410G>C",
"hgvs_p": "p.Arg137Pro",
"transcript": "NM_001204398.1",
"protein_id": "NP_001191327.1",
"transcript_support_level": null,
"aa_start": 137,
"aa_end": null,
"aa_length": 317,
"cds_start": 410,
"cds_end": null,
"cds_length": 954,
"cdna_start": 625,
"cdna_end": null,
"cdna_length": 1871,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PITX2",
"gene_hgnc_id": 9005,
"hgvs_c": "c.410G>C",
"hgvs_p": "p.Arg137Pro",
"transcript": "NM_153426.3",
"protein_id": "NP_700475.1",
"transcript_support_level": null,
"aa_start": 137,
"aa_end": null,
"aa_length": 317,
"cds_start": 410,
"cds_end": null,
"cds_length": 954,
"cdna_start": 651,
"cdna_end": null,
"cdna_length": 1897,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "P",
"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": "PITX2",
"gene_hgnc_id": 9005,
"hgvs_c": "c.410G>C",
"hgvs_p": "p.Arg137Pro",
"transcript": "ENST00000354925.6",
"protein_id": "ENSP00000347004.2",
"transcript_support_level": 2,
"aa_start": 137,
"aa_end": null,
"aa_length": 317,
"cds_start": 410,
"cds_end": null,
"cds_length": 954,
"cdna_start": 2116,
"cdna_end": null,
"cdna_length": 3359,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PITX2",
"gene_hgnc_id": 9005,
"hgvs_c": "c.410G>C",
"hgvs_p": "p.Arg137Pro",
"transcript": "ENST00000394595.8",
"protein_id": "ENSP00000378095.4",
"transcript_support_level": 5,
"aa_start": 137,
"aa_end": null,
"aa_length": 317,
"cds_start": 410,
"cds_end": null,
"cds_length": 954,
"cdna_start": 651,
"cdna_end": null,
"cdna_length": 1897,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "P",
"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": "PITX2",
"gene_hgnc_id": 9005,
"hgvs_c": "c.329G>C",
"hgvs_p": "p.Arg110Pro",
"transcript": "ENST00000614423.5",
"protein_id": "ENSP00000481951.2",
"transcript_support_level": 5,
"aa_start": 110,
"aa_end": null,
"aa_length": 290,
"cds_start": 329,
"cds_end": null,
"cds_length": 873,
"cdna_start": 473,
"cdna_end": null,
"cdna_length": 1718,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PITX2",
"gene_hgnc_id": 9005,
"hgvs_c": "c.410G>C",
"hgvs_p": "p.Arg137Pro",
"transcript": "ENST00000511837.5",
"protein_id": "ENSP00000421454.1",
"transcript_support_level": 5,
"aa_start": 137,
"aa_end": null,
"aa_length": 289,
"cds_start": 410,
"cds_end": null,
"cds_length": 870,
"cdna_start": 625,
"cdna_end": null,
"cdna_length": 1085,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "P",
"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": "PITX2",
"gene_hgnc_id": 9005,
"hgvs_c": "c.272G>C",
"hgvs_p": "p.Arg91Pro",
"transcript": "NM_001204399.1",
"protein_id": "NP_001191328.1",
"transcript_support_level": null,
"aa_start": 91,
"aa_end": null,
"aa_length": 271,
"cds_start": 272,
"cds_end": null,
"cds_length": 816,
"cdna_start": 487,
"cdna_end": null,
"cdna_length": 1733,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "P",
"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": "PITX2",
"gene_hgnc_id": 9005,
"hgvs_c": "c.272G>C",
"hgvs_p": "p.Arg91Pro",
"transcript": "NM_153427.3",
"protein_id": "NP_700476.1",
"transcript_support_level": null,
"aa_start": 91,
"aa_end": null,
"aa_length": 271,
"cds_start": 272,
"cds_end": null,
"cds_length": 816,
"cdna_start": 513,
"cdna_end": null,
"cdna_length": 1759,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "P",
"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": "PITX2",
"gene_hgnc_id": 9005,
"hgvs_c": "c.272G>C",
"hgvs_p": "p.Arg91Pro",
"transcript": "ENST00000511990.1",
"protein_id": "ENSP00000424142.1",
"transcript_support_level": 3,
"aa_start": 91,
"aa_end": null,
"aa_length": 117,
"cds_start": 272,
"cds_end": null,
"cds_length": 355,
"cdna_start": 380,
"cdna_end": null,
"cdna_length": 463,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PITX2",
"gene_hgnc_id": 9005,
"hgvs_c": "c.77G>C",
"hgvs_p": "p.Arg26Pro",
"transcript": "XM_024454090.2",
"protein_id": "XP_024309858.1",
"transcript_support_level": null,
"aa_start": 26,
"aa_end": null,
"aa_length": 206,
"cds_start": 77,
"cds_end": null,
"cds_length": 621,
"cdna_start": 261,
"cdna_end": null,
"cdna_length": 1507,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PITX2",
"gene_hgnc_id": 9005,
"hgvs_c": "c.204G>C",
"hgvs_p": "p.Ser68Ser",
"transcript": "ENST00000613094.5",
"protein_id": "ENSP00000484763.2",
"transcript_support_level": 5,
"aa_start": 68,
"aa_end": null,
"aa_length": 174,
"cds_start": 204,
"cds_end": null,
"cds_length": 525,
"cdna_start": 460,
"cdna_end": null,
"cdna_length": 1693,
"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": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PITX2",
"gene_hgnc_id": 9005,
"hgvs_c": "n.737G>C",
"hgvs_p": null,
"transcript": "ENST00000556049.1",
"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": 941,
"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": 1,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PITX2",
"gene_hgnc_id": 9005,
"hgvs_c": "n.158G>C",
"hgvs_p": null,
"transcript": "ENST00000607868.1",
"protein_id": null,
"transcript_support_level": 6,
"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": 1398,
"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": "PITX2",
"gene_hgnc_id": 9005,
"hgvs_c": "n.397G>C",
"hgvs_p": null,
"transcript": "ENST00000616641.5",
"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": 1139,
"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": "PITX2",
"gene_hgnc_id": 9005,
"hgvs_c": "n.401G>C",
"hgvs_p": null,
"transcript": "ENST00000644488.2",
"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": 1143,
"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": "PITX2",
"gene_hgnc_id": 9005,
"hgvs_c": "n.362G>C",
"hgvs_p": null,
"transcript": "ENST00000645131.1",
"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": 1608,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PITX2",
"gene_hgnc_id": 9005,
"dbsnp": "rs104893859",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9845118522644043,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.88,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9998,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.58,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.568,
"phylop100way_prediction": "Pathogenic",
"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": 18,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM1,PM2,PM5,PP3_Strong,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 18,
"benign_score": 0,
"pathogenic_score": 18,
"criteria": [
"PM1",
"PM2",
"PM5",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000644743.1",
"gene_symbol": "PITX2",
"hgnc_id": 9005,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,Unknown",
"hgvs_c": "c.431G>C",
"hgvs_p": "p.Arg144Pro"
}
],
"clinvar_disease": "Axenfeld-Rieger syndrome type 1,Inborn genetic diseases",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:1 LP:1",
"phenotype_combined": "Axenfeld-Rieger syndrome type 1|Inborn genetic diseases",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}