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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: 3-122284910-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=122284910&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 122284910,
"ref": "G",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000639785.2",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASR",
"gene_hgnc_id": 1514,
"hgvs_c": "c.2956G>T",
"hgvs_p": "p.Ala986Ser",
"transcript": "NM_000388.4",
"protein_id": "NP_000379.3",
"transcript_support_level": null,
"aa_start": 986,
"aa_end": null,
"aa_length": 1078,
"cds_start": 2956,
"cds_end": null,
"cds_length": 3237,
"cdna_start": 3343,
"cdna_end": null,
"cdna_length": 10062,
"mane_select": "ENST00000639785.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASR",
"gene_hgnc_id": 1514,
"hgvs_c": "c.2956G>T",
"hgvs_p": "p.Ala986Ser",
"transcript": "ENST00000639785.2",
"protein_id": "ENSP00000491584.2",
"transcript_support_level": 1,
"aa_start": 986,
"aa_end": null,
"aa_length": 1078,
"cds_start": 2956,
"cds_end": null,
"cds_length": 3237,
"cdna_start": 3343,
"cdna_end": null,
"cdna_length": 10062,
"mane_select": "NM_000388.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASR",
"gene_hgnc_id": 1514,
"hgvs_c": "c.2986G>T",
"hgvs_p": "p.Ala996Ser",
"transcript": "ENST00000498619.4",
"protein_id": "ENSP00000420194.1",
"transcript_support_level": 1,
"aa_start": 996,
"aa_end": null,
"aa_length": 1088,
"cds_start": 2986,
"cds_end": null,
"cds_length": 3267,
"cdna_start": 3424,
"cdna_end": null,
"cdna_length": 5009,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASR",
"gene_hgnc_id": 1514,
"hgvs_c": "c.2986G>T",
"hgvs_p": "p.Ala996Ser",
"transcript": "NM_001178065.2",
"protein_id": "NP_001171536.2",
"transcript_support_level": null,
"aa_start": 996,
"aa_end": null,
"aa_length": 1088,
"cds_start": 2986,
"cds_end": null,
"cds_length": 3267,
"cdna_start": 3431,
"cdna_end": null,
"cdna_length": 10150,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASR",
"gene_hgnc_id": 1514,
"hgvs_c": "c.2956G>T",
"hgvs_p": "p.Ala986Ser",
"transcript": "ENST00000638421.1",
"protein_id": "ENSP00000492190.1",
"transcript_support_level": 5,
"aa_start": 986,
"aa_end": null,
"aa_length": 1078,
"cds_start": 2956,
"cds_end": null,
"cds_length": 3237,
"cdna_start": 3495,
"cdna_end": null,
"cdna_length": 5088,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASR",
"gene_hgnc_id": 1514,
"hgvs_c": "c.2725G>T",
"hgvs_p": "p.Ala909Ser",
"transcript": "ENST00000490131.7",
"protein_id": "ENSP00000418685.2",
"transcript_support_level": 5,
"aa_start": 909,
"aa_end": null,
"aa_length": 1001,
"cds_start": 2725,
"cds_end": null,
"cds_length": 3006,
"cdna_start": 2967,
"cdna_end": null,
"cdna_length": 4015,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASR",
"gene_hgnc_id": 1514,
"hgvs_c": "c.2956G>T",
"hgvs_p": "p.Ala986Ser",
"transcript": "XM_006713789.4",
"protein_id": "XP_006713852.1",
"transcript_support_level": null,
"aa_start": 986,
"aa_end": null,
"aa_length": 1078,
"cds_start": 2956,
"cds_end": null,
"cds_length": 3237,
"cdna_start": 3401,
"cdna_end": null,
"cdna_length": 10120,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASR",
"gene_hgnc_id": 1514,
"hgvs_c": "c.2956G>T",
"hgvs_p": "p.Ala986Ser",
"transcript": "XM_017007324.2",
"protein_id": "XP_016862813.1",
"transcript_support_level": null,
"aa_start": 986,
"aa_end": null,
"aa_length": 1078,
"cds_start": 2956,
"cds_end": null,
"cds_length": 3237,
"cdna_start": 5275,
"cdna_end": null,
"cdna_length": 11994,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASR",
"gene_hgnc_id": 1514,
"hgvs_c": "c.2956G>T",
"hgvs_p": "p.Ala986Ser",
"transcript": "XM_017007325.2",
"protein_id": "XP_016862814.1",
"transcript_support_level": null,
"aa_start": 986,
"aa_end": null,
"aa_length": 1078,
"cds_start": 2956,
"cds_end": null,
"cds_length": 3237,
"cdna_start": 3300,
"cdna_end": null,
"cdna_length": 10019,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASR",
"gene_hgnc_id": 1514,
"hgvs_c": "c.2473G>T",
"hgvs_p": "p.Ala825Ser",
"transcript": "XM_047449065.1",
"protein_id": "XP_047305021.1",
"transcript_support_level": null,
"aa_start": 825,
"aa_end": null,
"aa_length": 917,
"cds_start": 2473,
"cds_end": null,
"cds_length": 2754,
"cdna_start": 3094,
"cdna_end": null,
"cdna_length": 9813,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "CASR",
"gene_hgnc_id": 1514,
"dbsnp": "rs1801725",
"frequency_reference_population": 0.13177666,
"hom_count_reference_population": 15629,
"allele_count_reference_population": 212692,
"gnomad_exomes_af": 0.134043,
"gnomad_genomes_af": 0.110008,
"gnomad_exomes_ac": 195949,
"gnomad_genomes_ac": 16743,
"gnomad_exomes_homalt": 14407,
"gnomad_genomes_homalt": 1222,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.0016186535358428955,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.287,
"revel_prediction": "Benign",
"alphamissense_score": 0.0781,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.26,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 3.227,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.01,
"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": -19,
"acmg_classification": "Benign",
"acmg_criteria": "PP2,BP4_Strong,BP6_Very_Strong,BA1",
"acmg_by_gene": [
{
"score": -19,
"benign_score": 20,
"pathogenic_score": 1,
"criteria": [
"PP2",
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000639785.2",
"gene_symbol": "CASR",
"hgnc_id": 1514,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.2956G>T",
"hgvs_p": "p.Ala986Ser"
}
],
"clinvar_disease": "Autosomal dominant hypocalcemia 1,Familial hypocalciuric hypercalcemia,Familial hypocalciuric hypercalcemia 1,Familial hypoparathyroidism,Malignant tumor of breast,Neonatal severe primary hyperparathyroidism,Nephrolithiasis/nephrocalcinosis,Serum calcium level,not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:12",
"phenotype_combined": "Serum calcium level|Familial hypocalciuric hypercalcemia 1|Familial hypoparathyroidism|Familial hypocalciuric hypercalcemia;Autosomal dominant hypocalcemia 1|not specified|Neonatal severe primary hyperparathyroidism|Autosomal dominant hypocalcemia 1|Malignant tumor of breast|not provided|Nephrolithiasis/nephrocalcinosis",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}