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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: 2-201629229-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=201629229&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 201629229,
"ref": "C",
"alt": "T",
"effect": "splice_donor_variant,intron_variant",
"transcript": "ENST00000409883.7",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "TMEM237",
"gene_hgnc_id": 14432,
"hgvs_c": "c.869+1G>A",
"hgvs_p": null,
"transcript": "NM_001044385.3",
"protein_id": "NP_001037850.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 408,
"cds_start": -4,
"cds_end": null,
"cds_length": 1227,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5399,
"mane_select": "ENST00000409883.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "TMEM237",
"gene_hgnc_id": 14432,
"hgvs_c": "c.869+1G>A",
"hgvs_p": null,
"transcript": "ENST00000409883.7",
"protein_id": "ENSP00000386264.2",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 408,
"cds_start": -4,
"cds_end": null,
"cds_length": 1227,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5399,
"mane_select": "NM_001044385.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "TMEM237",
"gene_hgnc_id": 14432,
"hgvs_c": "c.743+1G>A",
"hgvs_p": null,
"transcript": "ENST00000621467.5",
"protein_id": "ENSP00000480508.2",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 366,
"cds_start": -4,
"cds_end": null,
"cds_length": 1101,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5605,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "TMEM237",
"gene_hgnc_id": 14432,
"hgvs_c": "n.567+1G>A",
"hgvs_p": null,
"transcript": "ENST00000466641.5",
"protein_id": null,
"transcript_support_level": 1,
"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": 720,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "TMEM237",
"gene_hgnc_id": 14432,
"hgvs_c": "c.845+1G>A",
"hgvs_p": null,
"transcript": "NM_152388.4",
"protein_id": "NP_689601.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 400,
"cds_start": -4,
"cds_end": null,
"cds_length": 1203,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5316,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "TMEM237",
"gene_hgnc_id": 14432,
"hgvs_c": "c.845+1G>A",
"hgvs_p": null,
"transcript": "ENST00000409444.6",
"protein_id": "ENSP00000387203.2",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 400,
"cds_start": -4,
"cds_end": null,
"cds_length": 1203,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5592,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": 8,
"intron_rank_end": null,
"gene_symbol": "TMEM237",
"gene_hgnc_id": 14432,
"hgvs_c": "n.*433+1G>A",
"hgvs_p": null,
"transcript": "ENST00000286196.9",
"protein_id": "ENSP00000286196.5",
"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": 1805,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "TMEM237",
"gene_hgnc_id": 14432,
"hgvs_c": "n.737+1G>A",
"hgvs_p": null,
"transcript": "ENST00000466839.5",
"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": 839,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "TMEM237",
"gene_hgnc_id": 14432,
"hgvs_c": "n.759+1G>A",
"hgvs_p": null,
"transcript": "ENST00000471318.6",
"protein_id": null,
"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": 1591,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "TMEM237",
"gene_hgnc_id": 14432,
"hgvs_c": "n.809+1G>A",
"hgvs_p": null,
"transcript": "ENST00000686475.1",
"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": 5221,
"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": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM237",
"gene_hgnc_id": 14432,
"hgvs_c": "n.*669G>A",
"hgvs_p": null,
"transcript": "ENST00000432684.6",
"protein_id": "ENSP00000413230.2",
"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": 1071,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "TMEM237",
"gene_hgnc_id": 14432,
"dbsnp": "rs730882231",
"frequency_reference_population": 7.144123e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 7.14412e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.4300000071525574,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.949999988079071,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.43,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.552,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.96,
"spliceai_max_prediction": "Pathogenic",
"dbscsnv_ada_score": 0.999986675681007,
"dbscsnv_ada_prediction": "Pathogenic",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 14,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1_Strong,PM2,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 14,
"benign_score": 0,
"pathogenic_score": 14,
"criteria": [
"PVS1_Strong",
"PM2",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000409883.7",
"gene_symbol": "TMEM237",
"hgnc_id": 14432,
"effects": [
"splice_donor_variant",
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.869+1G>A",
"hgvs_p": null
}
],
"clinvar_disease": "Joubert syndrome 14,Meckel-Gruber syndrome",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:2 LP:1",
"phenotype_combined": "Meckel-Gruber syndrome|Joubert syndrome 14",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}