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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: 4-121825945-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=121825945&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 121825945,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000264499.9",
"consequences": [
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BBS7",
"gene_hgnc_id": 18758,
"hgvs_c": "c.2063A>G",
"hgvs_p": "p.Asn688Ser",
"transcript": "NM_176824.3",
"protein_id": "NP_789794.1",
"transcript_support_level": null,
"aa_start": 688,
"aa_end": null,
"aa_length": 715,
"cds_start": 2063,
"cds_end": null,
"cds_length": 2148,
"cdna_start": 2224,
"cdna_end": null,
"cdna_length": 3840,
"mane_select": "ENST00000264499.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BBS7",
"gene_hgnc_id": 18758,
"hgvs_c": "c.2063A>G",
"hgvs_p": "p.Asn688Ser",
"transcript": "ENST00000264499.9",
"protein_id": "ENSP00000264499.4",
"transcript_support_level": 1,
"aa_start": 688,
"aa_end": null,
"aa_length": 715,
"cds_start": 2063,
"cds_end": null,
"cds_length": 2148,
"cdna_start": 2224,
"cdna_end": null,
"cdna_length": 3840,
"mane_select": "NM_176824.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BBS7",
"gene_hgnc_id": 18758,
"hgvs_c": "c.332A>G",
"hgvs_p": "p.Asn111Ser",
"transcript": "ENST00000507814.5",
"protein_id": "ENSP00000423250.1",
"transcript_support_level": 3,
"aa_start": 111,
"aa_end": null,
"aa_length": 138,
"cds_start": 332,
"cds_end": null,
"cds_length": 417,
"cdna_start": 332,
"cdna_end": null,
"cdna_length": 734,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BBS7",
"gene_hgnc_id": 18758,
"hgvs_c": "c.2111A>G",
"hgvs_p": "p.Asn704Ser",
"transcript": "XM_011532079.4",
"protein_id": "XP_011530381.1",
"transcript_support_level": null,
"aa_start": 704,
"aa_end": null,
"aa_length": 731,
"cds_start": 2111,
"cds_end": null,
"cds_length": 2196,
"cdna_start": 2272,
"cdna_end": null,
"cdna_length": 3888,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BBS7",
"gene_hgnc_id": 18758,
"hgvs_c": "c.2108A>G",
"hgvs_p": "p.Asn703Ser",
"transcript": "XM_011532080.4",
"protein_id": "XP_011530382.1",
"transcript_support_level": null,
"aa_start": 703,
"aa_end": null,
"aa_length": 730,
"cds_start": 2108,
"cds_end": null,
"cds_length": 2193,
"cdna_start": 2269,
"cdna_end": null,
"cdna_length": 3885,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BBS7",
"gene_hgnc_id": 18758,
"hgvs_c": "c.2066A>G",
"hgvs_p": "p.Asn689Ser",
"transcript": "XM_005263106.5",
"protein_id": "XP_005263163.1",
"transcript_support_level": null,
"aa_start": 689,
"aa_end": null,
"aa_length": 716,
"cds_start": 2066,
"cds_end": null,
"cds_length": 2151,
"cdna_start": 2227,
"cdna_end": null,
"cdna_length": 3843,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BBS7",
"gene_hgnc_id": 18758,
"hgvs_c": "c.1946A>G",
"hgvs_p": "p.Asn649Ser",
"transcript": "XM_011532081.4",
"protein_id": "XP_011530383.1",
"transcript_support_level": null,
"aa_start": 649,
"aa_end": null,
"aa_length": 676,
"cds_start": 1946,
"cds_end": null,
"cds_length": 2031,
"cdna_start": 2107,
"cdna_end": null,
"cdna_length": 3723,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BBS7",
"gene_hgnc_id": 18758,
"hgvs_c": "c.1943A>G",
"hgvs_p": "p.Asn648Ser",
"transcript": "XM_047415889.1",
"protein_id": "XP_047271845.1",
"transcript_support_level": null,
"aa_start": 648,
"aa_end": null,
"aa_length": 675,
"cds_start": 1943,
"cds_end": null,
"cds_length": 2028,
"cdna_start": 2104,
"cdna_end": null,
"cdna_length": 3720,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BBS7",
"gene_hgnc_id": 18758,
"hgvs_c": "c.1901A>G",
"hgvs_p": "p.Asn634Ser",
"transcript": "XM_047415890.1",
"protein_id": "XP_047271846.1",
"transcript_support_level": null,
"aa_start": 634,
"aa_end": null,
"aa_length": 661,
"cds_start": 1901,
"cds_end": null,
"cds_length": 1986,
"cdna_start": 2062,
"cdna_end": null,
"cdna_length": 3678,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BBS7",
"gene_hgnc_id": 18758,
"hgvs_c": "c.1898A>G",
"hgvs_p": "p.Asn633Ser",
"transcript": "XM_017008357.3",
"protein_id": "XP_016863846.1",
"transcript_support_level": null,
"aa_start": 633,
"aa_end": null,
"aa_length": 660,
"cds_start": 1898,
"cds_end": null,
"cds_length": 1983,
"cdna_start": 2059,
"cdna_end": null,
"cdna_length": 3675,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "BBS7",
"gene_hgnc_id": 18758,
"dbsnp": "rs370656021",
"frequency_reference_population": 0.00014289939,
"hom_count_reference_population": 0,
"allele_count_reference_population": 230,
"gnomad_exomes_af": 0.000145471,
"gnomad_genomes_af": 0.000118273,
"gnomad_exomes_ac": 212,
"gnomad_genomes_ac": 18,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.3610585927963257,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.029999999329447746,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.385,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.1349,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.35,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 7.953,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.03,
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PP2,BP4",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 1,
"pathogenic_score": 1,
"criteria": [
"PP2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000264499.9",
"gene_symbol": "BBS7",
"hgnc_id": 18758,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2063A>G",
"hgvs_p": "p.Asn688Ser"
}
],
"clinvar_disease": "BBS7-related disorder,Bardet-Biedl syndrome,Bardet-Biedl syndrome 7,Inborn genetic diseases,not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:5",
"phenotype_combined": "Bardet-Biedl syndrome|not provided|Bardet-Biedl syndrome 7|BBS7-related disorder|Inborn genetic diseases",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}