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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: 11-61393964-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=11&pos=61393964&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "11",
"pos": 61393964,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_001173991.3",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM216",
"gene_hgnc_id": 25018,
"hgvs_c": "c.217C>T",
"hgvs_p": "p.Arg73Cys",
"transcript": "NM_001173990.3",
"protein_id": "NP_001167461.1",
"transcript_support_level": null,
"aa_start": 73,
"aa_end": null,
"aa_length": 145,
"cds_start": 217,
"cds_end": null,
"cds_length": 438,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000515837.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001173990.3"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM216",
"gene_hgnc_id": 25018,
"hgvs_c": "c.217C>T",
"hgvs_p": "p.Arg73Cys",
"transcript": "ENST00000515837.7",
"protein_id": "ENSP00000440638.1",
"transcript_support_level": 2,
"aa_start": 73,
"aa_end": null,
"aa_length": 145,
"cds_start": 217,
"cds_end": null,
"cds_length": 438,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001173990.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000515837.7"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM216",
"gene_hgnc_id": 25018,
"hgvs_c": "c.217C>T",
"hgvs_p": "p.Arg73Cys",
"transcript": "ENST00000334888.10",
"protein_id": "ENSP00000334844.5",
"transcript_support_level": 2,
"aa_start": 73,
"aa_end": null,
"aa_length": 148,
"cds_start": 217,
"cds_end": null,
"cds_length": 447,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000334888.10"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM216",
"gene_hgnc_id": 25018,
"hgvs_c": "c.34C>T",
"hgvs_p": "p.Arg12Cys",
"transcript": "ENST00000398979.7",
"protein_id": "ENSP00000381950.3",
"transcript_support_level": 1,
"aa_start": 12,
"aa_end": null,
"aa_length": 84,
"cds_start": 34,
"cds_end": null,
"cds_length": 255,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000398979.7"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_premature_start_codon_gain_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM216",
"gene_hgnc_id": 25018,
"hgvs_c": "c.-43C>T",
"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": null,
"cds_end": null,
"cds_length": 180,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000688959.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM216",
"gene_hgnc_id": 25018,
"hgvs_c": "c.217C>T",
"hgvs_p": "p.Arg73Cys",
"transcript": "NM_001173991.3",
"protein_id": "NP_001167462.1",
"transcript_support_level": null,
"aa_start": 73,
"aa_end": null,
"aa_length": 148,
"cds_start": 217,
"cds_end": null,
"cds_length": 447,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001173991.3"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM216",
"gene_hgnc_id": 25018,
"hgvs_c": "c.115C>T",
"hgvs_p": "p.Arg39Cys",
"transcript": "ENST00000909596.1",
"protein_id": "ENSP00000579655.1",
"transcript_support_level": null,
"aa_start": 39,
"aa_end": null,
"aa_length": 114,
"cds_start": 115,
"cds_end": null,
"cds_length": 345,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000909596.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM216",
"gene_hgnc_id": 25018,
"hgvs_c": "c.34C>T",
"hgvs_p": "p.Arg12Cys",
"transcript": "NM_016499.6",
"protein_id": "NP_057583.2",
"transcript_support_level": null,
"aa_start": 12,
"aa_end": null,
"aa_length": 87,
"cds_start": 34,
"cds_end": null,
"cds_length": 264,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_016499.6"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM216",
"gene_hgnc_id": 25018,
"hgvs_c": "c.34C>T",
"hgvs_p": "p.Arg12Cys",
"transcript": "NM_001330285.2",
"protein_id": "NP_001317214.1",
"transcript_support_level": null,
"aa_start": 12,
"aa_end": null,
"aa_length": 84,
"cds_start": 34,
"cds_end": null,
"cds_length": 255,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001330285.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM216",
"gene_hgnc_id": 25018,
"hgvs_c": "c.-43C>T",
"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": null,
"cds_end": null,
"cds_length": 180,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000688959.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"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": "TMEM216",
"gene_hgnc_id": 25018,
"hgvs_c": "n.231C>T",
"hgvs_p": null,
"transcript": "ENST00000541473.1",
"protein_id": null,
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000541473.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM216",
"gene_hgnc_id": 25018,
"hgvs_c": "n.494C>T",
"hgvs_p": null,
"transcript": "ENST00000544795.6",
"protein_id": null,
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000544795.6"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM216",
"gene_hgnc_id": 25018,
"hgvs_c": "n.233C>T",
"hgvs_p": null,
"transcript": "ENST00000684926.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000684926.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM216",
"gene_hgnc_id": 25018,
"hgvs_c": "n.217C>T",
"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": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000690736.1"
}
],
"gene_symbol": "TMEM216",
"gene_hgnc_id": 25018,
"dbsnp": "rs779526456",
"frequency_reference_population": 0.0000116310575,
"hom_count_reference_population": 0,
"allele_count_reference_population": 17,
"gnomad_exomes_af": 0.0000116311,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 17,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9571652412414551,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.728,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.4195,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.47,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 0.928,
"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": 11,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM1,PM2,PM5,PP3_Strong,PP5",
"acmg_by_gene": [
{
"score": 11,
"benign_score": 0,
"pathogenic_score": 11,
"criteria": [
"PM1",
"PM2",
"PM5",
"PP3_Strong",
"PP5"
],
"verdict": "Pathogenic",
"transcript": "NM_001173991.3",
"gene_symbol": "TMEM216",
"hgnc_id": 25018,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.217C>T",
"hgvs_p": "p.Arg73Cys"
}
],
"clinvar_disease": "Abnormality of the nervous system,Joubert syndrome,Joubert syndrome 2,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "P:2 LP:3 US:1",
"phenotype_combined": "Joubert syndrome 2|not provided|Joubert syndrome|Abnormality of the nervous system",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}