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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: 11-36593428-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=11&pos=36593428&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "11",
"pos": 36593428,
"ref": "C",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "ENST00000311485.8",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAG2",
"gene_hgnc_id": 9832,
"hgvs_c": "c.741G>A",
"hgvs_p": "p.Val247Val",
"transcript": "NM_000536.4",
"protein_id": "NP_000527.2",
"transcript_support_level": null,
"aa_start": 247,
"aa_end": null,
"aa_length": 527,
"cds_start": 741,
"cds_end": null,
"cds_length": 1584,
"cdna_start": 903,
"cdna_end": null,
"cdna_length": 2388,
"mane_select": "ENST00000311485.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAG2",
"gene_hgnc_id": 9832,
"hgvs_c": "c.741G>A",
"hgvs_p": "p.Val247Val",
"transcript": "ENST00000311485.8",
"protein_id": "ENSP00000308620.4",
"transcript_support_level": 1,
"aa_start": 247,
"aa_end": null,
"aa_length": 527,
"cds_start": 741,
"cds_end": null,
"cds_length": 1584,
"cdna_start": 903,
"cdna_end": null,
"cdna_length": 2388,
"mane_select": "NM_000536.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAG2",
"gene_hgnc_id": 9832,
"hgvs_c": "c.741G>A",
"hgvs_p": "p.Val247Val",
"transcript": "NM_001243785.2",
"protein_id": "NP_001230714.1",
"transcript_support_level": null,
"aa_start": 247,
"aa_end": null,
"aa_length": 527,
"cds_start": 741,
"cds_end": null,
"cds_length": 1584,
"cdna_start": 1098,
"cdna_end": null,
"cdna_length": 2583,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAG2",
"gene_hgnc_id": 9832,
"hgvs_c": "c.741G>A",
"hgvs_p": "p.Val247Val",
"transcript": "NM_001243786.2",
"protein_id": "NP_001230715.1",
"transcript_support_level": null,
"aa_start": 247,
"aa_end": null,
"aa_length": 527,
"cds_start": 741,
"cds_end": null,
"cds_length": 1584,
"cdna_start": 1292,
"cdna_end": null,
"cdna_length": 2777,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAG2",
"gene_hgnc_id": 9832,
"hgvs_c": "c.741G>A",
"hgvs_p": "p.Val247Val",
"transcript": "ENST00000527033.6",
"protein_id": "ENSP00000436895.2",
"transcript_support_level": 4,
"aa_start": 247,
"aa_end": null,
"aa_length": 527,
"cds_start": 741,
"cds_end": null,
"cds_length": 1584,
"cdna_start": 1098,
"cdna_end": null,
"cdna_length": 1941,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAG2",
"gene_hgnc_id": 9832,
"hgvs_c": "c.741G>A",
"hgvs_p": "p.Val247Val",
"transcript": "ENST00000529083.2",
"protein_id": "ENSP00000436327.2",
"transcript_support_level": 3,
"aa_start": 247,
"aa_end": null,
"aa_length": 527,
"cds_start": 741,
"cds_end": null,
"cds_length": 1584,
"cdna_start": 861,
"cdna_end": null,
"cdna_length": 1704,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAG2",
"gene_hgnc_id": 9832,
"hgvs_c": "c.741G>A",
"hgvs_p": "p.Val247Val",
"transcript": "ENST00000532616.2",
"protein_id": "ENSP00000432174.2",
"transcript_support_level": 4,
"aa_start": 247,
"aa_end": null,
"aa_length": 527,
"cds_start": 741,
"cds_end": null,
"cds_length": 1584,
"cdna_start": 1292,
"cdna_end": null,
"cdna_length": 2135,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAG2",
"gene_hgnc_id": 9832,
"hgvs_c": "c.741G>A",
"hgvs_p": "p.Val247Val",
"transcript": "XM_047427385.1",
"protein_id": "XP_047283341.1",
"transcript_support_level": null,
"aa_start": 247,
"aa_end": null,
"aa_length": 527,
"cds_start": 741,
"cds_end": null,
"cds_length": 1584,
"cdna_start": 1903,
"cdna_end": null,
"cdna_length": 4335,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAG2",
"gene_hgnc_id": 9832,
"hgvs_c": "c.741G>A",
"hgvs_p": "p.Val247Val",
"transcript": "XM_047427386.1",
"protein_id": "XP_047283342.1",
"transcript_support_level": null,
"aa_start": 247,
"aa_end": null,
"aa_length": 527,
"cds_start": 741,
"cds_end": null,
"cds_length": 1584,
"cdna_start": 4198,
"cdna_end": null,
"cdna_length": 5683,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "RAG2",
"gene_hgnc_id": 9832,
"hgvs_c": "n.131+4674G>A",
"hgvs_p": null,
"transcript": "ENST00000524423.1",
"protein_id": null,
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 529,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "RAG2",
"gene_hgnc_id": 9832,
"dbsnp": "rs34092949",
"frequency_reference_population": 0.0033252623,
"hom_count_reference_population": 161,
"allele_count_reference_population": 5367,
"gnomad_exomes_af": 0.00183552,
"gnomad_genomes_af": 0.0176233,
"gnomad_exomes_ac": 2683,
"gnomad_genomes_ac": 2684,
"gnomad_exomes_homalt": 84,
"gnomad_genomes_homalt": 77,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.550000011920929,
"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": -0.55,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.078,
"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,BA1",
"acmg_by_gene": [
{
"score": -21,
"benign_score": 21,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000311485.8",
"gene_symbol": "RAG2",
"hgnc_id": 9832,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.741G>A",
"hgvs_p": "p.Val247Val"
}
],
"clinvar_disease": " B cell-negative, NK cell-positive, T cell-negative, autosomal recessive,Combined immunodeficiency with skin granulomas,Histiocytic medullary reticulosis,Severe combined immunodeficiency,not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:5",
"phenotype_combined": "not specified|Severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-negative, NK cell-positive|Histiocytic medullary reticulosis|Severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-negative, NK cell-positive;Combined immunodeficiency with skin granulomas|not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}