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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: 12-123690539-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=123690539&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 123690539,
"ref": "C",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "ENST00000303372.7",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TCTN2",
"gene_hgnc_id": 25774,
"hgvs_c": "c.898C>T",
"hgvs_p": "p.Leu300Leu",
"transcript": "NM_024809.5",
"protein_id": "NP_079085.2",
"transcript_support_level": null,
"aa_start": 300,
"aa_end": null,
"aa_length": 697,
"cds_start": 898,
"cds_end": null,
"cds_length": 2094,
"cdna_start": 1026,
"cdna_end": null,
"cdna_length": 2908,
"mane_select": "ENST00000303372.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TCTN2",
"gene_hgnc_id": 25774,
"hgvs_c": "c.898C>T",
"hgvs_p": "p.Leu300Leu",
"transcript": "ENST00000303372.7",
"protein_id": "ENSP00000304941.5",
"transcript_support_level": 1,
"aa_start": 300,
"aa_end": null,
"aa_length": 697,
"cds_start": 898,
"cds_end": null,
"cds_length": 2094,
"cdna_start": 1026,
"cdna_end": null,
"cdna_length": 2908,
"mane_select": "NM_024809.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_premature_start_codon_gain_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TCTN2",
"gene_hgnc_id": 25774,
"hgvs_c": "c.-15C>T",
"hgvs_p": null,
"transcript": "XM_047429553.1",
"protein_id": "XP_047285509.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 393,
"cds_start": -4,
"cds_end": null,
"cds_length": 1182,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1980,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TCTN2",
"gene_hgnc_id": 25774,
"hgvs_c": "c.895C>T",
"hgvs_p": "p.Leu299Leu",
"transcript": "NM_001143850.3",
"protein_id": "NP_001137322.1",
"transcript_support_level": null,
"aa_start": 299,
"aa_end": null,
"aa_length": 696,
"cds_start": 895,
"cds_end": null,
"cds_length": 2091,
"cdna_start": 1023,
"cdna_end": null,
"cdna_length": 2905,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TCTN2",
"gene_hgnc_id": 25774,
"hgvs_c": "c.895C>T",
"hgvs_p": "p.Leu299Leu",
"transcript": "ENST00000426174.6",
"protein_id": "ENSP00000395171.2",
"transcript_support_level": 2,
"aa_start": 299,
"aa_end": null,
"aa_length": 696,
"cds_start": 895,
"cds_end": null,
"cds_length": 2091,
"cdna_start": 1023,
"cdna_end": null,
"cdna_length": 2513,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TCTN2",
"gene_hgnc_id": 25774,
"hgvs_c": "c.895C>T",
"hgvs_p": "p.Leu299Leu",
"transcript": "ENST00000679504.1",
"protein_id": "ENSP00000505006.1",
"transcript_support_level": null,
"aa_start": 299,
"aa_end": null,
"aa_length": 669,
"cds_start": 895,
"cds_end": null,
"cds_length": 2010,
"cdna_start": 1023,
"cdna_end": null,
"cdna_length": 2246,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TCTN2",
"gene_hgnc_id": 25774,
"hgvs_c": "c.898C>T",
"hgvs_p": "p.Leu300Leu",
"transcript": "NM_001410989.1",
"protein_id": "NP_001397918.1",
"transcript_support_level": null,
"aa_start": 300,
"aa_end": null,
"aa_length": 652,
"cds_start": 898,
"cds_end": null,
"cds_length": 1959,
"cdna_start": 1026,
"cdna_end": null,
"cdna_length": 2773,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TCTN2",
"gene_hgnc_id": 25774,
"hgvs_c": "c.898C>T",
"hgvs_p": "p.Leu300Leu",
"transcript": "ENST00000680574.1",
"protein_id": "ENSP00000505356.1",
"transcript_support_level": null,
"aa_start": 300,
"aa_end": null,
"aa_length": 652,
"cds_start": 898,
"cds_end": null,
"cds_length": 1959,
"cdna_start": 1029,
"cdna_end": null,
"cdna_length": 2374,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TCTN2",
"gene_hgnc_id": 25774,
"hgvs_c": "c.895C>T",
"hgvs_p": "p.Leu299Leu",
"transcript": "XM_017019974.2",
"protein_id": "XP_016875463.1",
"transcript_support_level": null,
"aa_start": 299,
"aa_end": null,
"aa_length": 651,
"cds_start": 895,
"cds_end": null,
"cds_length": 1956,
"cdna_start": 1023,
"cdna_end": null,
"cdna_length": 2770,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TCTN2",
"gene_hgnc_id": 25774,
"hgvs_c": "n.898C>T",
"hgvs_p": null,
"transcript": "ENST00000680500.1",
"protein_id": "ENSP00000506438.1",
"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": 2497,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TCTN2",
"gene_hgnc_id": 25774,
"hgvs_c": "c.-15C>T",
"hgvs_p": null,
"transcript": "XM_047429553.1",
"protein_id": "XP_047285509.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 393,
"cds_start": -4,
"cds_end": null,
"cds_length": 1182,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1980,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "TCTN2",
"gene_hgnc_id": 25774,
"dbsnp": "rs77804131",
"frequency_reference_population": 0.016780224,
"hom_count_reference_population": 319,
"allele_count_reference_population": 27086,
"gnomad_exomes_af": 0.0173739,
"gnomad_genomes_af": 0.0110821,
"gnomad_exomes_ac": 25398,
"gnomad_genomes_ac": 1688,
"gnomad_exomes_homalt": 305,
"gnomad_genomes_homalt": 14,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.38999998569488525,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.39,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.054,
"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": -19,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Moderate,BP6_Very_Strong,BP7,BS1,BS2",
"acmg_by_gene": [
{
"score": -19,
"benign_score": 19,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6_Very_Strong",
"BP7",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000303372.7",
"gene_symbol": "TCTN2",
"hgnc_id": 25774,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.898C>T",
"hgvs_p": "p.Leu300Leu"
}
],
"clinvar_disease": " type 8,Joubert syndrome,Joubert syndrome 24,Meckel syndrome,Meckel-Gruber syndrome,not provided,not specified",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:2 B:4",
"phenotype_combined": "not specified|Joubert syndrome;Meckel-Gruber syndrome|Joubert syndrome 24|Meckel syndrome, type 8|not provided",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}