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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: 7-41965975-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=7&pos=41965975&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "7",
"pos": 41965975,
"ref": "G",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000395925.8",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GLI3",
"gene_hgnc_id": 4319,
"hgvs_c": "c.3098C>A",
"hgvs_p": "p.Pro1033Gln",
"transcript": "NM_000168.6",
"protein_id": "NP_000159.3",
"transcript_support_level": null,
"aa_start": 1033,
"aa_end": null,
"aa_length": 1580,
"cds_start": 3098,
"cds_end": null,
"cds_length": 4743,
"cdna_start": 3379,
"cdna_end": null,
"cdna_length": 8405,
"mane_select": "ENST00000395925.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GLI3",
"gene_hgnc_id": 4319,
"hgvs_c": "c.3098C>A",
"hgvs_p": "p.Pro1033Gln",
"transcript": "ENST00000395925.8",
"protein_id": "ENSP00000379258.3",
"transcript_support_level": 5,
"aa_start": 1033,
"aa_end": null,
"aa_length": 1580,
"cds_start": 3098,
"cds_end": null,
"cds_length": 4743,
"cdna_start": 3379,
"cdna_end": null,
"cdna_length": 8405,
"mane_select": "NM_000168.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GLI3",
"gene_hgnc_id": 4319,
"hgvs_c": "c.3098C>A",
"hgvs_p": "p.Pro1033Gln",
"transcript": "ENST00000677605.1",
"protein_id": "ENSP00000503743.1",
"transcript_support_level": null,
"aa_start": 1033,
"aa_end": null,
"aa_length": 1580,
"cds_start": 3098,
"cds_end": null,
"cds_length": 4743,
"cdna_start": 3197,
"cdna_end": null,
"cdna_length": 8223,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GLI3",
"gene_hgnc_id": 4319,
"hgvs_c": "c.3098C>A",
"hgvs_p": "p.Pro1033Gln",
"transcript": "ENST00000678429.1",
"protein_id": "ENSP00000502957.1",
"transcript_support_level": null,
"aa_start": 1033,
"aa_end": null,
"aa_length": 1580,
"cds_start": 3098,
"cds_end": null,
"cds_length": 4743,
"cdna_start": 3211,
"cdna_end": null,
"cdna_length": 8237,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GLI3",
"gene_hgnc_id": 4319,
"hgvs_c": "c.2924C>A",
"hgvs_p": "p.Pro975Gln",
"transcript": "ENST00000677288.1",
"protein_id": "ENSP00000503986.1",
"transcript_support_level": null,
"aa_start": 975,
"aa_end": null,
"aa_length": 1522,
"cds_start": 2924,
"cds_end": null,
"cds_length": 4569,
"cdna_start": 3055,
"cdna_end": null,
"cdna_length": 8081,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GLI3",
"gene_hgnc_id": 4319,
"hgvs_c": "c.2921C>A",
"hgvs_p": "p.Pro974Gln",
"transcript": "ENST00000479210.1",
"protein_id": "ENSP00000496377.1",
"transcript_support_level": 2,
"aa_start": 974,
"aa_end": null,
"aa_length": 1521,
"cds_start": 2921,
"cds_end": null,
"cds_length": 4566,
"cdna_start": 3075,
"cdna_end": null,
"cdna_length": 4968,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GLI3",
"gene_hgnc_id": 4319,
"hgvs_c": "c.3098C>A",
"hgvs_p": "p.Pro1033Gln",
"transcript": "XM_047420205.1",
"protein_id": "XP_047276161.1",
"transcript_support_level": null,
"aa_start": 1033,
"aa_end": null,
"aa_length": 1580,
"cds_start": 3098,
"cds_end": null,
"cds_length": 4743,
"cdna_start": 3298,
"cdna_end": null,
"cdna_length": 8324,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GLI3",
"gene_hgnc_id": 4319,
"hgvs_c": "c.3098C>A",
"hgvs_p": "p.Pro1033Gln",
"transcript": "XM_047420206.1",
"protein_id": "XP_047276162.1",
"transcript_support_level": null,
"aa_start": 1033,
"aa_end": null,
"aa_length": 1580,
"cds_start": 3098,
"cds_end": null,
"cds_length": 4743,
"cdna_start": 11229,
"cdna_end": null,
"cdna_length": 16255,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GLI3",
"gene_hgnc_id": 4319,
"hgvs_c": "c.3098C>A",
"hgvs_p": "p.Pro1033Gln",
"transcript": "XM_047420207.1",
"protein_id": "XP_047276163.1",
"transcript_support_level": null,
"aa_start": 1033,
"aa_end": null,
"aa_length": 1580,
"cds_start": 3098,
"cds_end": null,
"cds_length": 4743,
"cdna_start": 3261,
"cdna_end": null,
"cdna_length": 8287,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GLI3",
"gene_hgnc_id": 4319,
"hgvs_c": "c.3098C>A",
"hgvs_p": "p.Pro1033Gln",
"transcript": "XM_047420208.1",
"protein_id": "XP_047276164.1",
"transcript_support_level": null,
"aa_start": 1033,
"aa_end": null,
"aa_length": 1580,
"cds_start": 3098,
"cds_end": null,
"cds_length": 4743,
"cdna_start": 3415,
"cdna_end": null,
"cdna_length": 8441,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GLI3",
"gene_hgnc_id": 4319,
"hgvs_c": "c.3098C>A",
"hgvs_p": "p.Pro1033Gln",
"transcript": "XM_047420209.1",
"protein_id": "XP_047276165.1",
"transcript_support_level": null,
"aa_start": 1033,
"aa_end": null,
"aa_length": 1580,
"cds_start": 3098,
"cds_end": null,
"cds_length": 4743,
"cdna_start": 3229,
"cdna_end": null,
"cdna_length": 8255,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GLI3",
"gene_hgnc_id": 4319,
"hgvs_c": "c.3095C>A",
"hgvs_p": "p.Pro1032Gln",
"transcript": "XM_017011997.2",
"protein_id": "XP_016867486.1",
"transcript_support_level": null,
"aa_start": 1032,
"aa_end": null,
"aa_length": 1579,
"cds_start": 3095,
"cds_end": null,
"cds_length": 4740,
"cdna_start": 13070,
"cdna_end": null,
"cdna_length": 18096,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GLI3",
"gene_hgnc_id": 4319,
"hgvs_c": "c.2921C>A",
"hgvs_p": "p.Pro974Gln",
"transcript": "XM_011515274.3",
"protein_id": "XP_011513576.1",
"transcript_support_level": null,
"aa_start": 974,
"aa_end": null,
"aa_length": 1521,
"cds_start": 2921,
"cds_end": null,
"cds_length": 4566,
"cdna_start": 3075,
"cdna_end": null,
"cdna_length": 8101,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "GLI3",
"gene_hgnc_id": 4319,
"dbsnp": "rs376956433",
"frequency_reference_population": 0.00005725552,
"hom_count_reference_population": 0,
"allele_count_reference_population": 92,
"gnomad_exomes_af": 0.0000591186,
"gnomad_genomes_af": 0.00003944,
"gnomad_exomes_ac": 86,
"gnomad_genomes_ac": 6,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.127992182970047,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.116,
"revel_prediction": "Benign",
"alphamissense_score": 0.1003,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.56,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.851,
"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": -7,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Moderate,BP6,BS1",
"acmg_by_gene": [
{
"score": -7,
"benign_score": 7,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6",
"BS1"
],
"verdict": "Benign",
"transcript": "ENST00000395925.8",
"gene_symbol": "GLI3",
"hgnc_id": 4319,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.3098C>A",
"hgvs_p": "p.Pro1033Gln"
}
],
"clinvar_disease": "Greig cephalopolysyndactyly syndrome,Inborn genetic diseases,Pallister-Hall syndrome,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:2 LB:2",
"phenotype_combined": "not specified|Greig cephalopolysyndactyly syndrome;Pallister-Hall syndrome|Inborn genetic diseases",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}