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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: 7-41965989-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=7&pos=41965989&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "7",
"pos": 41965989,
"ref": "G",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "NM_000168.6",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_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.3084C>T",
"hgvs_p": "p.Ser1028Ser",
"transcript": "NM_000168.6",
"protein_id": "NP_000159.3",
"transcript_support_level": null,
"aa_start": 1028,
"aa_end": null,
"aa_length": 1580,
"cds_start": 3084,
"cds_end": null,
"cds_length": 4743,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000395925.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_000168.6"
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_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.3084C>T",
"hgvs_p": "p.Ser1028Ser",
"transcript": "ENST00000395925.8",
"protein_id": "ENSP00000379258.3",
"transcript_support_level": 5,
"aa_start": 1028,
"aa_end": null,
"aa_length": 1580,
"cds_start": 3084,
"cds_end": null,
"cds_length": 4743,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_000168.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000395925.8"
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_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.3084C>T",
"hgvs_p": "p.Ser1028Ser",
"transcript": "ENST00000677605.1",
"protein_id": "ENSP00000503743.1",
"transcript_support_level": null,
"aa_start": 1028,
"aa_end": null,
"aa_length": 1580,
"cds_start": 3084,
"cds_end": null,
"cds_length": 4743,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000677605.1"
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_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.3084C>T",
"hgvs_p": "p.Ser1028Ser",
"transcript": "ENST00000678429.1",
"protein_id": "ENSP00000502957.1",
"transcript_support_level": null,
"aa_start": 1028,
"aa_end": null,
"aa_length": 1580,
"cds_start": 3084,
"cds_end": null,
"cds_length": 4743,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000678429.1"
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_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.3084C>T",
"hgvs_p": "p.Ser1028Ser",
"transcript": "ENST00000878750.1",
"protein_id": "ENSP00000548809.1",
"transcript_support_level": null,
"aa_start": 1028,
"aa_end": null,
"aa_length": 1580,
"cds_start": 3084,
"cds_end": null,
"cds_length": 4743,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000878750.1"
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_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.3084C>T",
"hgvs_p": "p.Ser1028Ser",
"transcript": "ENST00000878751.1",
"protein_id": "ENSP00000548810.1",
"transcript_support_level": null,
"aa_start": 1028,
"aa_end": null,
"aa_length": 1580,
"cds_start": 3084,
"cds_end": null,
"cds_length": 4743,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000878751.1"
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_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.3054C>T",
"hgvs_p": "p.Ser1018Ser",
"transcript": "ENST00000911414.1",
"protein_id": "ENSP00000581473.1",
"transcript_support_level": null,
"aa_start": 1018,
"aa_end": null,
"aa_length": 1570,
"cds_start": 3054,
"cds_end": null,
"cds_length": 4713,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000911414.1"
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_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.2910C>T",
"hgvs_p": "p.Ser970Ser",
"transcript": "ENST00000677288.1",
"protein_id": "ENSP00000503986.1",
"transcript_support_level": null,
"aa_start": 970,
"aa_end": null,
"aa_length": 1522,
"cds_start": 2910,
"cds_end": null,
"cds_length": 4569,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000677288.1"
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_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.2907C>T",
"hgvs_p": "p.Ser969Ser",
"transcript": "ENST00000479210.1",
"protein_id": "ENSP00000496377.1",
"transcript_support_level": 2,
"aa_start": 969,
"aa_end": null,
"aa_length": 1521,
"cds_start": 2907,
"cds_end": null,
"cds_length": 4566,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000479210.1"
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_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.3084C>T",
"hgvs_p": "p.Ser1028Ser",
"transcript": "XM_047420205.1",
"protein_id": "XP_047276161.1",
"transcript_support_level": null,
"aa_start": 1028,
"aa_end": null,
"aa_length": 1580,
"cds_start": 3084,
"cds_end": null,
"cds_length": 4743,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047420205.1"
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_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.3084C>T",
"hgvs_p": "p.Ser1028Ser",
"transcript": "XM_047420206.1",
"protein_id": "XP_047276162.1",
"transcript_support_level": null,
"aa_start": 1028,
"aa_end": null,
"aa_length": 1580,
"cds_start": 3084,
"cds_end": null,
"cds_length": 4743,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047420206.1"
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_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.3084C>T",
"hgvs_p": "p.Ser1028Ser",
"transcript": "XM_047420207.1",
"protein_id": "XP_047276163.1",
"transcript_support_level": null,
"aa_start": 1028,
"aa_end": null,
"aa_length": 1580,
"cds_start": 3084,
"cds_end": null,
"cds_length": 4743,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047420207.1"
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_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.3084C>T",
"hgvs_p": "p.Ser1028Ser",
"transcript": "XM_047420208.1",
"protein_id": "XP_047276164.1",
"transcript_support_level": null,
"aa_start": 1028,
"aa_end": null,
"aa_length": 1580,
"cds_start": 3084,
"cds_end": null,
"cds_length": 4743,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047420208.1"
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_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.3084C>T",
"hgvs_p": "p.Ser1028Ser",
"transcript": "XM_047420209.1",
"protein_id": "XP_047276165.1",
"transcript_support_level": null,
"aa_start": 1028,
"aa_end": null,
"aa_length": 1580,
"cds_start": 3084,
"cds_end": null,
"cds_length": 4743,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047420209.1"
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_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.3081C>T",
"hgvs_p": "p.Ser1027Ser",
"transcript": "XM_017011997.2",
"protein_id": "XP_016867486.1",
"transcript_support_level": null,
"aa_start": 1027,
"aa_end": null,
"aa_length": 1579,
"cds_start": 3081,
"cds_end": null,
"cds_length": 4740,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017011997.2"
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_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.2907C>T",
"hgvs_p": "p.Ser969Ser",
"transcript": "XM_011515274.3",
"protein_id": "XP_011513576.1",
"transcript_support_level": null,
"aa_start": 969,
"aa_end": null,
"aa_length": 1521,
"cds_start": 2907,
"cds_end": null,
"cds_length": 4566,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011515274.3"
}
],
"gene_symbol": "GLI3",
"gene_hgnc_id": 4319,
"dbsnp": "rs79703713",
"frequency_reference_population": 0.01865125,
"hom_count_reference_population": 348,
"allele_count_reference_population": 29925,
"gnomad_exomes_af": 0.0192948,
"gnomad_genomes_af": 0.0125151,
"gnomad_exomes_ac": 28019,
"gnomad_genomes_ac": 1906,
"gnomad_exomes_homalt": 327,
"gnomad_genomes_homalt": 21,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.5400000214576721,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.54,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.524,
"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": -21,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BS1,BS2",
"acmg_by_gene": [
{
"score": -21,
"benign_score": 21,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_000168.6",
"gene_symbol": "GLI3",
"hgnc_id": 4319,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.3084C>T",
"hgvs_p": "p.Ser1028Ser"
}
],
"clinvar_disease": "Greig cephalopolysyndactyly syndrome,Pallister-Hall syndrome,Polydactyly,not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:6",
"phenotype_combined": "Polydactyly|not specified|Pallister-Hall syndrome|Greig cephalopolysyndactyly syndrome|not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}