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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: 2-233309201-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=233309201&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 233309201,
"ref": "C",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "NM_000541.5",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SAG",
"gene_hgnc_id": 10521,
"hgvs_c": "c.12C>T",
"hgvs_p": "p.Ser4Ser",
"transcript": "NM_000541.5",
"protein_id": "NP_000532.2",
"transcript_support_level": null,
"aa_start": 4,
"aa_end": null,
"aa_length": 405,
"cds_start": 12,
"cds_end": null,
"cds_length": 1218,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000409110.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_000541.5"
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SAG",
"gene_hgnc_id": 10521,
"hgvs_c": "c.12C>T",
"hgvs_p": "p.Ser4Ser",
"transcript": "ENST00000409110.6",
"protein_id": "ENSP00000386444.1",
"transcript_support_level": 5,
"aa_start": 4,
"aa_end": null,
"aa_length": 405,
"cds_start": 12,
"cds_end": null,
"cds_length": 1218,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_000541.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000409110.6"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SAG",
"gene_hgnc_id": 10521,
"hgvs_c": "n.144+1179C>T",
"hgvs_p": null,
"transcript": "ENST00000462487.5",
"protein_id": null,
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000462487.5"
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SAG",
"gene_hgnc_id": 10521,
"hgvs_c": "c.12C>T",
"hgvs_p": "p.Ser4Ser",
"transcript": "ENST00000447536.5",
"protein_id": "ENSP00000408937.1",
"transcript_support_level": 3,
"aa_start": 4,
"aa_end": null,
"aa_length": 168,
"cds_start": 12,
"cds_end": null,
"cds_length": 507,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000447536.5"
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SAG",
"gene_hgnc_id": 10521,
"hgvs_c": "c.12C>T",
"hgvs_p": "p.Ser4Ser",
"transcript": "ENST00000415974.1",
"protein_id": "ENSP00000409475.1",
"transcript_support_level": 2,
"aa_start": 4,
"aa_end": null,
"aa_length": 129,
"cds_start": 12,
"cds_end": null,
"cds_length": 390,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000415974.1"
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SAG",
"gene_hgnc_id": 10521,
"hgvs_c": "c.12C>T",
"hgvs_p": "p.Ser4Ser",
"transcript": "XM_017004641.2",
"protein_id": "XP_016860130.1",
"transcript_support_level": null,
"aa_start": 4,
"aa_end": null,
"aa_length": 373,
"cds_start": 12,
"cds_end": null,
"cds_length": 1122,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017004641.2"
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SAG",
"gene_hgnc_id": 10521,
"hgvs_c": "c.12C>T",
"hgvs_p": "p.Ser4Ser",
"transcript": "XM_017004642.2",
"protein_id": "XP_016860131.1",
"transcript_support_level": null,
"aa_start": 4,
"aa_end": null,
"aa_length": 369,
"cds_start": 12,
"cds_end": null,
"cds_length": 1110,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017004642.2"
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SAG",
"gene_hgnc_id": 10521,
"hgvs_c": "c.12C>T",
"hgvs_p": "p.Ser4Ser",
"transcript": "XM_017004643.2",
"protein_id": "XP_016860132.1",
"transcript_support_level": null,
"aa_start": 4,
"aa_end": null,
"aa_length": 273,
"cds_start": 12,
"cds_end": null,
"cds_length": 822,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017004643.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SAG",
"gene_hgnc_id": 10521,
"hgvs_c": "n.131C>T",
"hgvs_p": null,
"transcript": "ENST00000412969.6",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000412969.6"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SAG",
"gene_hgnc_id": 10521,
"hgvs_c": "n.12C>T",
"hgvs_p": null,
"transcript": "ENST00000453143.5",
"protein_id": "ENSP00000404733.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000453143.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SAG",
"gene_hgnc_id": 10521,
"hgvs_c": "n.183C>T",
"hgvs_p": null,
"transcript": "ENST00000471884.5",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000471884.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SAG",
"gene_hgnc_id": 10521,
"hgvs_c": "n.247C>T",
"hgvs_p": null,
"transcript": "ENST00000476500.5",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000476500.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SAG",
"gene_hgnc_id": 10521,
"hgvs_c": "n.40C>T",
"hgvs_p": null,
"transcript": "XR_001738882.2",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "XR_001738882.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SAG",
"gene_hgnc_id": 10521,
"hgvs_c": "n.139+1179C>T",
"hgvs_p": null,
"transcript": "ENST00000479450.1",
"protein_id": null,
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000479450.1"
}
],
"gene_symbol": "SAG",
"gene_hgnc_id": 10521,
"dbsnp": "rs1700011294",
"frequency_reference_population": 0.000006818593,
"hom_count_reference_population": 0,
"allele_count_reference_population": 11,
"gnomad_exomes_af": 0.00000615959,
"gnomad_genomes_af": 0.0000131492,
"gnomad_exomes_ac": 9,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.6899999976158142,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.029999999329447746,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.69,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.946,
"phylop100way_prediction": "Benign",
"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": -6,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Strong,BP6,BP7",
"acmg_by_gene": [
{
"score": -6,
"benign_score": 6,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BP7"
],
"verdict": "Likely_benign",
"transcript": "NM_000541.5",
"gene_symbol": "SAG",
"hgnc_id": 10521,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.12C>T",
"hgvs_p": "p.Ser4Ser"
}
],
"clinvar_disease": "Retinal dystrophy,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:1",
"phenotype_combined": "not provided|Retinal dystrophy",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}