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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: 7-42148252-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=7&pos=42148252&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 20,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "GLI3",
"hgnc_id": 4319,
"hgvs_c": "c.341G>A",
"hgvs_p": "p.Arg114Lys",
"inheritance_mode": "AD,AR",
"pathogenic_score": 0,
"score": -20,
"transcript": "NM_000168.6",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BS1,BS2",
"acmg_score": -20,
"allele_count_reference_population": 6895,
"alphamissense_prediction": null,
"alphamissense_score": 0.3482,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Uncertain_significance",
"bayesdelnoaf_score": -0.07,
"chr": "7",
"clinvar_classification": "Benign/Likely benign",
"clinvar_disease": " postaxial, type A1,GLI3-related disorder,Greig cephalopolysyndactyly syndrome,Pallister-Hall syndrome,Polydactyly,Polysyndactyly 4,not provided,not specified",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:6 B:6",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.014516115188598633,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 1580,
"aa_ref": "R",
"aa_start": 114,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8405,
"cdna_start": 622,
"cds_end": null,
"cds_length": 4743,
"cds_start": 341,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "NM_000168.6",
"gene_hgnc_id": 4319,
"gene_symbol": "GLI3",
"hgvs_c": "c.341G>A",
"hgvs_p": "p.Arg114Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000395925.8",
"protein_coding": true,
"protein_id": "NP_000159.3",
"strand": false,
"transcript": "NM_000168.6",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 1580,
"aa_ref": "R",
"aa_start": 114,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 8405,
"cdna_start": 622,
"cds_end": null,
"cds_length": 4743,
"cds_start": 341,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000395925.8",
"gene_hgnc_id": 4319,
"gene_symbol": "GLI3",
"hgvs_c": "c.341G>A",
"hgvs_p": "p.Arg114Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_000168.6",
"protein_coding": true,
"protein_id": "ENSP00000379258.3",
"strand": false,
"transcript": "ENST00000395925.8",
"transcript_support_level": 5
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 1580,
"aa_ref": "R",
"aa_start": 114,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8223,
"cdna_start": 440,
"cds_end": null,
"cds_length": 4743,
"cds_start": 341,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000677605.1",
"gene_hgnc_id": 4319,
"gene_symbol": "GLI3",
"hgvs_c": "c.341G>A",
"hgvs_p": "p.Arg114Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000503743.1",
"strand": false,
"transcript": "ENST00000677605.1",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 1580,
"aa_ref": "R",
"aa_start": 114,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8237,
"cdna_start": 454,
"cds_end": null,
"cds_length": 4743,
"cds_start": 341,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000678429.1",
"gene_hgnc_id": 4319,
"gene_symbol": "GLI3",
"hgvs_c": "c.341G>A",
"hgvs_p": "p.Arg114Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000502957.1",
"strand": false,
"transcript": "ENST00000678429.1",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 1580,
"aa_ref": "R",
"aa_start": 114,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5373,
"cdna_start": 655,
"cds_end": null,
"cds_length": 4743,
"cds_start": 341,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000878750.1",
"gene_hgnc_id": 4319,
"gene_symbol": "GLI3",
"hgvs_c": "c.341G>A",
"hgvs_p": "p.Arg114Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000548809.1",
"strand": false,
"transcript": "ENST00000878750.1",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 1580,
"aa_ref": "R",
"aa_start": 114,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5220,
"cdna_start": 553,
"cds_end": null,
"cds_length": 4743,
"cds_start": 341,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000878751.1",
"gene_hgnc_id": 4319,
"gene_symbol": "GLI3",
"hgvs_c": "c.341G>A",
"hgvs_p": "p.Arg114Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000548810.1",
"strand": false,
"transcript": "ENST00000878751.1",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 1570,
"aa_ref": "R",
"aa_start": 114,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8342,
"cdna_start": 595,
"cds_end": null,
"cds_length": 4713,
"cds_start": 341,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000911414.1",
"gene_hgnc_id": 4319,
"gene_symbol": "GLI3",
"hgvs_c": "c.341G>A",
"hgvs_p": "p.Arg114Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000581473.1",
"strand": false,
"transcript": "ENST00000911414.1",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 1522,
"aa_ref": "R",
"aa_start": 55,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8081,
"cdna_start": 295,
"cds_end": null,
"cds_length": 4569,
"cds_start": 164,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000677288.1",
"gene_hgnc_id": 4319,
"gene_symbol": "GLI3",
"hgvs_c": "c.164G>A",
"hgvs_p": "p.Arg55Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000503986.1",
"strand": false,
"transcript": "ENST00000677288.1",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 1521,
"aa_ref": "R",
"aa_start": 55,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4968,
"cdna_start": 318,
"cds_end": null,
"cds_length": 4566,
"cds_start": 164,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000479210.1",
"gene_hgnc_id": 4319,
"gene_symbol": "GLI3",
"hgvs_c": "c.164G>A",
"hgvs_p": "p.Arg55Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000496377.1",
"strand": false,
"transcript": "ENST00000479210.1",
"transcript_support_level": 2
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 79,
"aa_ref": "R",
"aa_start": 55,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 683,
"cdna_start": 368,
"cds_end": null,
"cds_length": 240,
"cds_start": 164,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000647255.1",
"gene_hgnc_id": 4319,
"gene_symbol": "GLI3",
"hgvs_c": "c.164G>A",
"hgvs_p": "p.Arg55Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000495745.1",
"strand": false,
"transcript": "ENST00000647255.1",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 70,
"aa_ref": "R",
"aa_start": 55,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 615,
"cdna_start": 449,
"cds_end": null,
"cds_length": 213,
"cds_start": 164,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000642432.1",
"gene_hgnc_id": 4319,
"gene_symbol": "GLI3",
"hgvs_c": "c.164G>A",
"hgvs_p": "p.Arg55Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000495498.1",
"strand": false,
"transcript": "ENST00000642432.1",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 1580,
"aa_ref": "R",
"aa_start": 114,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8324,
"cdna_start": 541,
"cds_end": null,
"cds_length": 4743,
"cds_start": 341,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "XM_047420205.1",
"gene_hgnc_id": 4319,
"gene_symbol": "GLI3",
"hgvs_c": "c.341G>A",
"hgvs_p": "p.Arg114Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047276161.1",
"strand": false,
"transcript": "XM_047420205.1",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 1580,
"aa_ref": "R",
"aa_start": 114,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 16255,
"cdna_start": 8472,
"cds_end": null,
"cds_length": 4743,
"cds_start": 341,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "XM_047420206.1",
"gene_hgnc_id": 4319,
"gene_symbol": "GLI3",
"hgvs_c": "c.341G>A",
"hgvs_p": "p.Arg114Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047276162.1",
"strand": false,
"transcript": "XM_047420206.1",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 1580,
"aa_ref": "R",
"aa_start": 114,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8287,
"cdna_start": 504,
"cds_end": null,
"cds_length": 4743,
"cds_start": 341,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "XM_047420207.1",
"gene_hgnc_id": 4319,
"gene_symbol": "GLI3",
"hgvs_c": "c.341G>A",
"hgvs_p": "p.Arg114Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047276163.1",
"strand": false,
"transcript": "XM_047420207.1",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 1580,
"aa_ref": "R",
"aa_start": 114,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8441,
"cdna_start": 658,
"cds_end": null,
"cds_length": 4743,
"cds_start": 341,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "XM_047420208.1",
"gene_hgnc_id": 4319,
"gene_symbol": "GLI3",
"hgvs_c": "c.341G>A",
"hgvs_p": "p.Arg114Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047276164.1",
"strand": false,
"transcript": "XM_047420208.1",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 1580,
"aa_ref": "R",
"aa_start": 114,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8255,
"cdna_start": 472,
"cds_end": null,
"cds_length": 4743,
"cds_start": 341,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "XM_047420209.1",
"gene_hgnc_id": 4319,
"gene_symbol": "GLI3",
"hgvs_c": "c.341G>A",
"hgvs_p": "p.Arg114Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047276165.1",
"strand": false,
"transcript": "XM_047420209.1",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 1579,
"aa_ref": "R",
"aa_start": 113,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 18096,
"cdna_start": 10313,
"cds_end": null,
"cds_length": 4740,
"cds_start": 338,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "XM_017011997.2",
"gene_hgnc_id": 4319,
"gene_symbol": "GLI3",
"hgvs_c": "c.338G>A",
"hgvs_p": "p.Arg113Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016867486.1",
"strand": false,
"transcript": "XM_017011997.2",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 1521,
"aa_ref": "R",
"aa_start": 55,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8101,
"cdna_start": 318,
"cds_end": null,
"cds_length": 4566,
"cds_start": 164,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "XM_011515274.3",
"gene_hgnc_id": 4319,
"gene_symbol": "GLI3",
"hgvs_c": "c.164G>A",
"hgvs_p": "p.Arg55Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011513576.1",
"strand": false,
"transcript": "XM_011515274.3",
"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": 1821,
"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": "ENST00000643264.1",
"gene_hgnc_id": 4319,
"gene_symbol": "GLI3",
"hgvs_c": "n.164G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000495207.1",
"strand": false,
"transcript": "ENST00000643264.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs146458902",
"effect": "missense_variant",
"frequency_reference_population": 0.0042766267,
"gene_hgnc_id": 4319,
"gene_symbol": "GLI3",
"gnomad_exomes_ac": 6498,
"gnomad_exomes_af": 0.00445017,
"gnomad_exomes_homalt": 17,
"gnomad_genomes_ac": 397,
"gnomad_genomes_af": 0.0026104,
"gnomad_genomes_homalt": 1,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 18,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Benign/Likely benign",
"phenotype_combined": "Polydactyly|Pallister-Hall syndrome|Greig cephalopolysyndactyly syndrome|not specified|not provided|Greig cephalopolysyndactyly syndrome;Pallister-Hall syndrome|Polydactyly, postaxial, type A1;Polysyndactyly 4;Greig cephalopolysyndactyly syndrome;Pallister-Hall syndrome|GLI3-related disorder",
"phylop100way_prediction": "Pathogenic",
"phylop100way_score": 7.542,
"pos": 42148252,
"ref": "C",
"revel_prediction": "Pathogenic",
"revel_score": 0.719,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_000168.6"
}
]
}