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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: 3-122284631-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=122284631&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 1,
"criteria": [
"PM1",
"PP2",
"BP4"
],
"effects": [
"missense_variant"
],
"gene_symbol": "CASR",
"hgnc_id": 1514,
"hgvs_c": "c.2707A>G",
"hgvs_p": "p.Asn903Asp",
"inheritance_mode": "AD,AR",
"pathogenic_score": 3,
"score": 2,
"transcript": "NM_001178065.2",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM1,PP2,BP4",
"acmg_score": 2,
"allele_count_reference_population": 6,
"alphamissense_prediction": null,
"alphamissense_score": 0.1234,
"alt": "G",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.24,
"chr": "3",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": " 8, idiopathic generalized, susceptibility to,Autosomal dominant hypocalcemia 1,Epilepsy,Familial hypocalciuric hypercalcemia,Familial hypocalciuric hypercalcemia 1,Neonatal severe primary hyperparathyroidism,Nephrolithiasis/nephrocalcinosis",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:3",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.3450676202774048,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "D",
"aa_end": null,
"aa_length": 1078,
"aa_ref": "N",
"aa_start": 893,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 10062,
"cdna_start": 3064,
"cds_end": null,
"cds_length": 3237,
"cds_start": 2677,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "NM_000388.4",
"gene_hgnc_id": 1514,
"gene_symbol": "CASR",
"hgvs_c": "c.2677A>G",
"hgvs_p": "p.Asn893Asp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000639785.2",
"protein_coding": true,
"protein_id": "NP_000379.3",
"strand": true,
"transcript": "NM_000388.4",
"transcript_support_level": null
},
{
"aa_alt": "D",
"aa_end": null,
"aa_length": 1078,
"aa_ref": "N",
"aa_start": 893,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 10062,
"cdna_start": 3064,
"cds_end": null,
"cds_length": 3237,
"cds_start": 2677,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000639785.2",
"gene_hgnc_id": 1514,
"gene_symbol": "CASR",
"hgvs_c": "c.2677A>G",
"hgvs_p": "p.Asn893Asp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_000388.4",
"protein_coding": true,
"protein_id": "ENSP00000491584.2",
"strand": true,
"transcript": "ENST00000639785.2",
"transcript_support_level": 1
},
{
"aa_alt": "D",
"aa_end": null,
"aa_length": 1088,
"aa_ref": "N",
"aa_start": 903,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5009,
"cdna_start": 3145,
"cds_end": null,
"cds_length": 3267,
"cds_start": 2707,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000498619.4",
"gene_hgnc_id": 1514,
"gene_symbol": "CASR",
"hgvs_c": "c.2707A>G",
"hgvs_p": "p.Asn903Asp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000420194.1",
"strand": true,
"transcript": "ENST00000498619.4",
"transcript_support_level": 1
},
{
"aa_alt": "D",
"aa_end": null,
"aa_length": 1088,
"aa_ref": "N",
"aa_start": 903,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 10150,
"cdna_start": 3152,
"cds_end": null,
"cds_length": 3267,
"cds_start": 2707,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "NM_001178065.2",
"gene_hgnc_id": 1514,
"gene_symbol": "CASR",
"hgvs_c": "c.2707A>G",
"hgvs_p": "p.Asn903Asp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001171536.2",
"strand": true,
"transcript": "NM_001178065.2",
"transcript_support_level": null
},
{
"aa_alt": "D",
"aa_end": null,
"aa_length": 1078,
"aa_ref": "N",
"aa_start": 893,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5088,
"cdna_start": 3216,
"cds_end": null,
"cds_length": 3237,
"cds_start": 2677,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000638421.1",
"gene_hgnc_id": 1514,
"gene_symbol": "CASR",
"hgvs_c": "c.2677A>G",
"hgvs_p": "p.Asn893Asp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000492190.1",
"strand": true,
"transcript": "ENST00000638421.1",
"transcript_support_level": 5
},
{
"aa_alt": "D",
"aa_end": null,
"aa_length": 1078,
"aa_ref": "N",
"aa_start": 893,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4980,
"cdna_start": 3117,
"cds_end": null,
"cds_length": 3237,
"cds_start": 2677,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000851099.1",
"gene_hgnc_id": 1514,
"gene_symbol": "CASR",
"hgvs_c": "c.2677A>G",
"hgvs_p": "p.Asn893Asp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000521158.1",
"strand": true,
"transcript": "ENST00000851099.1",
"transcript_support_level": null
},
{
"aa_alt": "D",
"aa_end": null,
"aa_length": 1078,
"aa_ref": "N",
"aa_start": 893,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4986,
"cdna_start": 3123,
"cds_end": null,
"cds_length": 3237,
"cds_start": 2677,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000851100.1",
"gene_hgnc_id": 1514,
"gene_symbol": "CASR",
"hgvs_c": "c.2677A>G",
"hgvs_p": "p.Asn893Asp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000521159.1",
"strand": true,
"transcript": "ENST00000851100.1",
"transcript_support_level": null
},
{
"aa_alt": "D",
"aa_end": null,
"aa_length": 1001,
"aa_ref": "N",
"aa_start": 816,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4015,
"cdna_start": 2688,
"cds_end": null,
"cds_length": 3006,
"cds_start": 2446,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000490131.7",
"gene_hgnc_id": 1514,
"gene_symbol": "CASR",
"hgvs_c": "c.2446A>G",
"hgvs_p": "p.Asn816Asp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000418685.2",
"strand": true,
"transcript": "ENST00000490131.7",
"transcript_support_level": 5
},
{
"aa_alt": "D",
"aa_end": null,
"aa_length": 1078,
"aa_ref": "N",
"aa_start": 893,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 10120,
"cdna_start": 3122,
"cds_end": null,
"cds_length": 3237,
"cds_start": 2677,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "XM_006713789.4",
"gene_hgnc_id": 1514,
"gene_symbol": "CASR",
"hgvs_c": "c.2677A>G",
"hgvs_p": "p.Asn893Asp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_006713852.1",
"strand": true,
"transcript": "XM_006713789.4",
"transcript_support_level": null
},
{
"aa_alt": "D",
"aa_end": null,
"aa_length": 1078,
"aa_ref": "N",
"aa_start": 893,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 11994,
"cdna_start": 4996,
"cds_end": null,
"cds_length": 3237,
"cds_start": 2677,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "XM_017007324.2",
"gene_hgnc_id": 1514,
"gene_symbol": "CASR",
"hgvs_c": "c.2677A>G",
"hgvs_p": "p.Asn893Asp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016862813.1",
"strand": true,
"transcript": "XM_017007324.2",
"transcript_support_level": null
},
{
"aa_alt": "D",
"aa_end": null,
"aa_length": 1078,
"aa_ref": "N",
"aa_start": 893,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 10019,
"cdna_start": 3021,
"cds_end": null,
"cds_length": 3237,
"cds_start": 2677,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "XM_017007325.2",
"gene_hgnc_id": 1514,
"gene_symbol": "CASR",
"hgvs_c": "c.2677A>G",
"hgvs_p": "p.Asn893Asp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016862814.1",
"strand": true,
"transcript": "XM_017007325.2",
"transcript_support_level": null
},
{
"aa_alt": "D",
"aa_end": null,
"aa_length": 917,
"aa_ref": "N",
"aa_start": 732,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9813,
"cdna_start": 2815,
"cds_end": null,
"cds_length": 2754,
"cds_start": 2194,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "XM_047449065.1",
"gene_hgnc_id": 1514,
"gene_symbol": "CASR",
"hgvs_c": "c.2194A>G",
"hgvs_p": "p.Asn732Asp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047305021.1",
"strand": true,
"transcript": "XM_047449065.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs1392921552",
"effect": "missense_variant",
"frequency_reference_population": 0.000003717638,
"gene_hgnc_id": 1514,
"gene_symbol": "CASR",
"gnomad_exomes_ac": 4,
"gnomad_exomes_af": 0.00000273654,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 2,
"gnomad_genomes_af": 0.0000131384,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "Autosomal dominant hypocalcemia 1;Familial hypocalciuric hypercalcemia|Nephrolithiasis/nephrocalcinosis|Autosomal dominant hypocalcemia 1;Epilepsy, idiopathic generalized, susceptibility to, 8;Neonatal severe primary hyperparathyroidism;Familial hypocalciuric hypercalcemia 1",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 5.798,
"pos": 122284631,
"ref": "A",
"revel_prediction": "Uncertain_significance",
"revel_score": 0.384,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_001178065.2"
}
]
}