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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: 11-61393965-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=11&pos=61393965&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PS3",
"PM1",
"PM2",
"PM5",
"PP5_Very_Strong"
],
"effects": [
"missense_variant"
],
"gene_symbol": "TMEM216",
"hgnc_id": 25018,
"hgvs_c": "c.218G>T",
"hgvs_p": "p.Arg73Leu",
"inheritance_mode": "AR",
"pathogenic_score": 18,
"score": 18,
"transcript": "NM_001173991.3",
"verdict": "Pathogenic"
}
],
"acmg_classification": "Pathogenic",
"acmg_criteria": "PS3,PM1,PM2,PM5,PP5_Very_Strong",
"acmg_score": 18,
"allele_count_reference_population": 199,
"alphamissense_prediction": null,
"alphamissense_score": 0.8219,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.49,
"chr": "11",
"clinvar_classification": "Pathogenic",
"clinvar_disease": " type 2,Inborn genetic diseases,Joubert syndrome,Joubert syndrome 2,Meckel syndrome,TMEM216-related disorder,not provided",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:14 O:1",
"computational_prediction_selected": "Uncertain_significance",
"computational_score_selected": 0.5550619959831238,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 145,
"aa_ref": "R",
"aa_start": 73,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1053,
"cdna_start": 263,
"cds_end": null,
"cds_length": 438,
"cds_start": 218,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "NM_001173990.3",
"gene_hgnc_id": 25018,
"gene_symbol": "TMEM216",
"hgvs_c": "c.218G>T",
"hgvs_p": "p.Arg73Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000515837.7",
"protein_coding": true,
"protein_id": "NP_001167461.1",
"strand": true,
"transcript": "NM_001173990.3",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 145,
"aa_ref": "R",
"aa_start": 73,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 1053,
"cdna_start": 263,
"cds_end": null,
"cds_length": 438,
"cds_start": 218,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000515837.7",
"gene_hgnc_id": 25018,
"gene_symbol": "TMEM216",
"hgvs_c": "c.218G>T",
"hgvs_p": "p.Arg73Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001173990.3",
"protein_coding": true,
"protein_id": "ENSP00000440638.1",
"strand": true,
"transcript": "ENST00000515837.7",
"transcript_support_level": 2
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 148,
"aa_ref": "R",
"aa_start": 73,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 1062,
"cdna_start": 263,
"cds_end": null,
"cds_length": 447,
"cds_start": 218,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000334888.10",
"gene_hgnc_id": 25018,
"gene_symbol": "TMEM216",
"hgvs_c": "c.218G>T",
"hgvs_p": "p.Arg73Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000334844.5",
"strand": true,
"transcript": "ENST00000334888.10",
"transcript_support_level": 2
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 84,
"aa_ref": "R",
"aa_start": 12,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 908,
"cdna_start": 471,
"cds_end": null,
"cds_length": 255,
"cds_start": 35,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000398979.7",
"gene_hgnc_id": 25018,
"gene_symbol": "TMEM216",
"hgvs_c": "c.35G>T",
"hgvs_p": "p.Arg12Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000381950.3",
"strand": true,
"transcript": "ENST00000398979.7",
"transcript_support_level": 1
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 148,
"aa_ref": "R",
"aa_start": 73,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1062,
"cdna_start": 263,
"cds_end": null,
"cds_length": 447,
"cds_start": 218,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "NM_001173991.3",
"gene_hgnc_id": 25018,
"gene_symbol": "TMEM216",
"hgvs_c": "c.218G>T",
"hgvs_p": "p.Arg73Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001167462.1",
"strand": true,
"transcript": "NM_001173991.3",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 114,
"aa_ref": "R",
"aa_start": 39,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 943,
"cdna_start": 146,
"cds_end": null,
"cds_length": 345,
"cds_start": 116,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000909596.1",
"gene_hgnc_id": 25018,
"gene_symbol": "TMEM216",
"hgvs_c": "c.116G>T",
"hgvs_p": "p.Arg39Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000579655.1",
"strand": true,
"transcript": "ENST00000909596.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 87,
"aa_ref": "R",
"aa_start": 12,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1076,
"cdna_start": 277,
"cds_end": null,
"cds_length": 264,
"cds_start": 35,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "NM_016499.6",
"gene_hgnc_id": 25018,
"gene_symbol": "TMEM216",
"hgvs_c": "c.35G>T",
"hgvs_p": "p.Arg12Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_057583.2",
"strand": true,
"transcript": "NM_016499.6",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 84,
"aa_ref": "R",
"aa_start": 12,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1067,
"cdna_start": 277,
"cds_end": null,
"cds_length": 255,
"cds_start": 35,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "NM_001330285.2",
"gene_hgnc_id": 25018,
"gene_symbol": "TMEM216",
"hgvs_c": "c.35G>T",
"hgvs_p": "p.Arg12Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001317214.1",
"strand": true,
"transcript": "NM_001330285.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 59,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 940,
"cdna_start": null,
"cds_end": null,
"cds_length": 180,
"cds_start": null,
"consequences": [
"5_prime_UTR_variant"
],
"exon_count": 5,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000688959.1",
"gene_hgnc_id": 25018,
"gene_symbol": "TMEM216",
"hgvs_c": "c.-42G>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000509213.1",
"strand": true,
"transcript": "ENST00000688959.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 568,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000541473.1",
"gene_hgnc_id": 25018,
"gene_symbol": "TMEM216",
"hgvs_c": "n.232G>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000541473.1",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 1351,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000544795.6",
"gene_hgnc_id": 25018,
"gene_symbol": "TMEM216",
"hgvs_c": "n.495G>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000544795.6",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 1090,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000684926.1",
"gene_hgnc_id": 25018,
"gene_symbol": "TMEM216",
"hgvs_c": "n.234G>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000684926.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 1099,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000690736.1",
"gene_hgnc_id": 25018,
"gene_symbol": "TMEM216",
"hgvs_c": "n.218G>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000508542.1",
"strand": true,
"transcript": "ENST00000690736.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs201108965",
"effect": "missense_variant",
"frequency_reference_population": 0.00012331511,
"gene_hgnc_id": 25018,
"gene_symbol": "TMEM216",
"gnomad_exomes_ac": 179,
"gnomad_exomes_af": 0.000122468,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 20,
"gnomad_genomes_af": 0.000131453,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Pathogenic",
"phenotype_combined": "Joubert syndrome 2|Meckel syndrome, type 2|not provided|Joubert syndrome|Inborn genetic diseases|TMEM216-related disorder|Joubert syndrome 2;Meckel syndrome, type 2",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 6.698,
"pos": 61393965,
"ref": "G",
"revel_prediction": "Pathogenic",
"revel_score": 0.804,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_001173991.3"
}
]
}