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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: 11-61397797-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=11&pos=61397797&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "11",
"pos": 61397797,
"ref": "C",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "ENST00000334888.10",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM216",
"gene_hgnc_id": 25018,
"hgvs_c": "c.253C>A",
"hgvs_p": "p.Arg85Arg",
"transcript": "NM_001173990.3",
"protein_id": "NP_001167461.1",
"transcript_support_level": null,
"aa_start": 85,
"aa_end": null,
"aa_length": 145,
"cds_start": 253,
"cds_end": null,
"cds_length": 438,
"cdna_start": 298,
"cdna_end": null,
"cdna_length": 1053,
"mane_select": "ENST00000515837.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM216",
"gene_hgnc_id": 25018,
"hgvs_c": "c.253C>A",
"hgvs_p": "p.Arg85Arg",
"transcript": "ENST00000515837.7",
"protein_id": "ENSP00000440638.1",
"transcript_support_level": 2,
"aa_start": 85,
"aa_end": null,
"aa_length": 145,
"cds_start": 253,
"cds_end": null,
"cds_length": 438,
"cdna_start": 298,
"cdna_end": null,
"cdna_length": 1053,
"mane_select": "NM_001173990.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM216",
"gene_hgnc_id": 25018,
"hgvs_c": "c.253C>A",
"hgvs_p": "p.Arg85Arg",
"transcript": "ENST00000334888.10",
"protein_id": "ENSP00000334844.5",
"transcript_support_level": 2,
"aa_start": 85,
"aa_end": null,
"aa_length": 148,
"cds_start": 253,
"cds_end": null,
"cds_length": 447,
"cdna_start": 298,
"cdna_end": null,
"cdna_length": 1062,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM216",
"gene_hgnc_id": 25018,
"hgvs_c": "c.70C>A",
"hgvs_p": "p.Arg24Arg",
"transcript": "ENST00000398979.7",
"protein_id": "ENSP00000381950.3",
"transcript_support_level": 1,
"aa_start": 24,
"aa_end": null,
"aa_length": 84,
"cds_start": 70,
"cds_end": null,
"cds_length": 255,
"cdna_start": 506,
"cdna_end": null,
"cdna_length": 908,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM216",
"gene_hgnc_id": 25018,
"hgvs_c": "c.253C>A",
"hgvs_p": "p.Arg85Arg",
"transcript": "NM_001173991.3",
"protein_id": "NP_001167462.1",
"transcript_support_level": null,
"aa_start": 85,
"aa_end": null,
"aa_length": 148,
"cds_start": 253,
"cds_end": null,
"cds_length": 447,
"cdna_start": 298,
"cdna_end": null,
"cdna_length": 1062,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM216",
"gene_hgnc_id": 25018,
"hgvs_c": "c.70C>A",
"hgvs_p": "p.Arg24Arg",
"transcript": "NM_016499.6",
"protein_id": "NP_057583.2",
"transcript_support_level": null,
"aa_start": 24,
"aa_end": null,
"aa_length": 87,
"cds_start": 70,
"cds_end": null,
"cds_length": 264,
"cdna_start": 312,
"cdna_end": null,
"cdna_length": 1076,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM216",
"gene_hgnc_id": 25018,
"hgvs_c": "c.70C>A",
"hgvs_p": "p.Arg24Arg",
"transcript": "NM_001330285.2",
"protein_id": "NP_001317214.1",
"transcript_support_level": null,
"aa_start": 24,
"aa_end": null,
"aa_length": 84,
"cds_start": 70,
"cds_end": null,
"cds_length": 255,
"cdna_start": 312,
"cdna_end": null,
"cdna_length": 1067,
"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": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM216",
"gene_hgnc_id": 25018,
"hgvs_c": "n.576C>A",
"hgvs_p": null,
"transcript": "ENST00000544795.6",
"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": 1351,
"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": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM216",
"gene_hgnc_id": 25018,
"hgvs_c": "n.315C>A",
"hgvs_p": null,
"transcript": "ENST00000684926.1",
"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": 1090,
"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": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM216",
"gene_hgnc_id": 25018,
"hgvs_c": "n.299C>A",
"hgvs_p": null,
"transcript": "ENST00000690736.1",
"protein_id": "ENSP00000508542.1",
"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": 1099,
"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": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM216",
"gene_hgnc_id": 25018,
"hgvs_c": "c.-6C>A",
"hgvs_p": null,
"transcript": "ENST00000688959.1",
"protein_id": "ENSP00000509213.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 59,
"cds_start": -4,
"cds_end": null,
"cds_length": 180,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 940,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "TMEM216",
"gene_hgnc_id": 25018,
"dbsnp": "rs11230683",
"frequency_reference_population": 0.00064890395,
"hom_count_reference_population": 27,
"allele_count_reference_population": 1047,
"gnomad_exomes_af": 0.000608418,
"gnomad_genomes_af": 0.00103726,
"gnomad_exomes_ac": 889,
"gnomad_genomes_ac": 158,
"gnomad_exomes_homalt": 22,
"gnomad_genomes_homalt": 5,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.36000001430511475,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.05000000074505806,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.36,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.258,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.05,
"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": "ENST00000334888.10",
"gene_symbol": "TMEM216",
"hgnc_id": 25018,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.253C>A",
"hgvs_p": "p.Arg85Arg"
}
],
"clinvar_disease": " type 2,Joubert syndrome,Joubert syndrome 2,Meckel syndrome,not provided,not specified",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:4 B:2",
"phenotype_combined": "not provided|not specified|Meckel syndrome, type 2|Joubert syndrome 2|Joubert syndrome",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}