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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: 12-123707685-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=123707685&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 123707685,
"ref": "G",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000303372.7",
"consequences": [
{
"aa_ref": "W",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TCTN2",
"gene_hgnc_id": 25774,
"hgvs_c": "c.2066G>C",
"hgvs_p": "p.Trp689Ser",
"transcript": "NM_024809.5",
"protein_id": "NP_079085.2",
"transcript_support_level": null,
"aa_start": 689,
"aa_end": null,
"aa_length": 697,
"cds_start": 2066,
"cds_end": null,
"cds_length": 2094,
"cdna_start": 2194,
"cdna_end": null,
"cdna_length": 2908,
"mane_select": "ENST00000303372.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TCTN2",
"gene_hgnc_id": 25774,
"hgvs_c": "c.2066G>C",
"hgvs_p": "p.Trp689Ser",
"transcript": "ENST00000303372.7",
"protein_id": "ENSP00000304941.5",
"transcript_support_level": 1,
"aa_start": 689,
"aa_end": null,
"aa_length": 697,
"cds_start": 2066,
"cds_end": null,
"cds_length": 2094,
"cdna_start": 2194,
"cdna_end": null,
"cdna_length": 2908,
"mane_select": "NM_024809.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TCTN2",
"gene_hgnc_id": 25774,
"hgvs_c": "c.2063G>C",
"hgvs_p": "p.Trp688Ser",
"transcript": "NM_001143850.3",
"protein_id": "NP_001137322.1",
"transcript_support_level": null,
"aa_start": 688,
"aa_end": null,
"aa_length": 696,
"cds_start": 2063,
"cds_end": null,
"cds_length": 2091,
"cdna_start": 2191,
"cdna_end": null,
"cdna_length": 2905,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TCTN2",
"gene_hgnc_id": 25774,
"hgvs_c": "c.2063G>C",
"hgvs_p": "p.Trp688Ser",
"transcript": "ENST00000426174.6",
"protein_id": "ENSP00000395171.2",
"transcript_support_level": 2,
"aa_start": 688,
"aa_end": null,
"aa_length": 696,
"cds_start": 2063,
"cds_end": null,
"cds_length": 2091,
"cdna_start": 2191,
"cdna_end": null,
"cdna_length": 2513,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TCTN2",
"gene_hgnc_id": 25774,
"hgvs_c": "c.1931G>C",
"hgvs_p": "p.Trp644Ser",
"transcript": "NM_001410989.1",
"protein_id": "NP_001397918.1",
"transcript_support_level": null,
"aa_start": 644,
"aa_end": null,
"aa_length": 652,
"cds_start": 1931,
"cds_end": null,
"cds_length": 1959,
"cdna_start": 2059,
"cdna_end": null,
"cdna_length": 2773,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TCTN2",
"gene_hgnc_id": 25774,
"hgvs_c": "c.1931G>C",
"hgvs_p": "p.Trp644Ser",
"transcript": "ENST00000680574.1",
"protein_id": "ENSP00000505356.1",
"transcript_support_level": null,
"aa_start": 644,
"aa_end": null,
"aa_length": 652,
"cds_start": 1931,
"cds_end": null,
"cds_length": 1959,
"cdna_start": 2062,
"cdna_end": null,
"cdna_length": 2374,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TCTN2",
"gene_hgnc_id": 25774,
"hgvs_c": "c.1928G>C",
"hgvs_p": "p.Trp643Ser",
"transcript": "XM_017019974.2",
"protein_id": "XP_016875463.1",
"transcript_support_level": null,
"aa_start": 643,
"aa_end": null,
"aa_length": 651,
"cds_start": 1928,
"cds_end": null,
"cds_length": 1956,
"cdna_start": 2056,
"cdna_end": null,
"cdna_length": 2770,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TCTN2",
"gene_hgnc_id": 25774,
"hgvs_c": "c.1154G>C",
"hgvs_p": "p.Trp385Ser",
"transcript": "XM_047429553.1",
"protein_id": "XP_047285509.1",
"transcript_support_level": null,
"aa_start": 385,
"aa_end": null,
"aa_length": 393,
"cds_start": 1154,
"cds_end": null,
"cds_length": 1182,
"cdna_start": 1266,
"cdna_end": null,
"cdna_length": 1980,
"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": "ENSG00000255839",
"gene_hgnc_id": null,
"hgvs_c": "n.238C>G",
"hgvs_p": null,
"transcript": "ENST00000538837.1",
"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": 321,
"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": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TCTN2",
"gene_hgnc_id": 25774,
"hgvs_c": "n.1167G>C",
"hgvs_p": null,
"transcript": "ENST00000680394.1",
"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": 1496,
"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": 19,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TCTN2",
"gene_hgnc_id": 25774,
"hgvs_c": "n.*438G>C",
"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": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TCTN2",
"gene_hgnc_id": 25774,
"hgvs_c": "n.*438G>C",
"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": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": 17,
"intron_rank_end": null,
"gene_symbol": "TCTN2",
"gene_hgnc_id": 25774,
"hgvs_c": "c.1982-519G>C",
"hgvs_p": null,
"transcript": "ENST00000679504.1",
"protein_id": "ENSP00000505006.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 669,
"cds_start": -4,
"cds_end": null,
"cds_length": 2010,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2246,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "TCTN2",
"gene_hgnc_id": 25774,
"dbsnp": "rs771335558",
"frequency_reference_population": 0.000006815323,
"hom_count_reference_population": 0,
"allele_count_reference_population": 11,
"gnomad_exomes_af": 0.00000410432,
"gnomad_genomes_af": 0.0000328653,
"gnomad_exomes_ac": 6,
"gnomad_genomes_ac": 5,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.7377206087112427,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.649,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.1775,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.09,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 6.686,
"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": 2,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000303372.7",
"gene_symbol": "TCTN2",
"hgnc_id": 25774,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2066G>C",
"hgvs_p": "p.Trp689Ser"
},
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000538837.1",
"gene_symbol": "ENSG00000255839",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.238C>G",
"hgvs_p": null
}
],
"clinvar_disease": " type 8,Inborn genetic diseases,Joubert syndrome,Joubert syndrome 24,Meckel syndrome,Meckel-Gruber syndrome",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:3",
"phenotype_combined": "Meckel-Gruber syndrome;Joubert syndrome|Meckel syndrome, type 8;Joubert syndrome 24|Inborn genetic diseases",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}