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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: 13-48345110-A-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=13&pos=48345110&ref=A&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "13",
"pos": 48345110,
"ref": "A",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000267163.6",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RB1",
"gene_hgnc_id": 9884,
"hgvs_c": "c.411A>T",
"hgvs_p": "p.Glu137Asp",
"transcript": "NM_000321.3",
"protein_id": "NP_000312.2",
"transcript_support_level": null,
"aa_start": 137,
"aa_end": null,
"aa_length": 928,
"cds_start": 411,
"cds_end": null,
"cds_length": 2787,
"cdna_start": 573,
"cdna_end": null,
"cdna_length": 4768,
"mane_select": "ENST00000267163.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RB1",
"gene_hgnc_id": 9884,
"hgvs_c": "c.411A>T",
"hgvs_p": "p.Glu137Asp",
"transcript": "ENST00000267163.6",
"protein_id": "ENSP00000267163.4",
"transcript_support_level": 1,
"aa_start": 137,
"aa_end": null,
"aa_length": 928,
"cds_start": 411,
"cds_end": null,
"cds_length": 2787,
"cdna_start": 573,
"cdna_end": null,
"cdna_length": 4768,
"mane_select": "NM_000321.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 22,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "RB1",
"gene_hgnc_id": 9884,
"hgvs_c": "n.138-14907A>T",
"hgvs_p": null,
"transcript": "ENST00000467505.6",
"protein_id": "ENSP00000434702.1",
"transcript_support_level": 1,
"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": 4274,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RB1",
"gene_hgnc_id": 9884,
"hgvs_c": "c.411A>T",
"hgvs_p": "p.Glu137Asp",
"transcript": "NM_001407165.1",
"protein_id": "NP_001394094.1",
"transcript_support_level": null,
"aa_start": 137,
"aa_end": null,
"aa_length": 923,
"cds_start": 411,
"cds_end": null,
"cds_length": 2772,
"cdna_start": 573,
"cdna_end": null,
"cdna_length": 4787,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RB1",
"gene_hgnc_id": 9884,
"hgvs_c": "c.411A>T",
"hgvs_p": "p.Glu137Asp",
"transcript": "ENST00000650461.1",
"protein_id": "ENSP00000497193.1",
"transcript_support_level": null,
"aa_start": 137,
"aa_end": null,
"aa_length": 923,
"cds_start": 411,
"cds_end": null,
"cds_length": 2772,
"cdna_start": 577,
"cdna_end": null,
"cdna_length": 4629,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RB1",
"gene_hgnc_id": 9884,
"hgvs_c": "c.411A>T",
"hgvs_p": "p.Glu137Asp",
"transcript": "ENST00000713858.1",
"protein_id": "ENSP00000519163.1",
"transcript_support_level": null,
"aa_start": 137,
"aa_end": null,
"aa_length": 893,
"cds_start": 411,
"cds_end": null,
"cds_length": 2682,
"cdna_start": 477,
"cdna_end": null,
"cdna_length": 4552,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RB1",
"gene_hgnc_id": 9884,
"hgvs_c": "c.411A>T",
"hgvs_p": "p.Glu137Asp",
"transcript": "ENST00000713857.1",
"protein_id": "ENSP00000519162.1",
"transcript_support_level": null,
"aa_start": 137,
"aa_end": null,
"aa_length": 877,
"cds_start": 411,
"cds_end": null,
"cds_length": 2634,
"cdna_start": 477,
"cdna_end": null,
"cdna_length": 4504,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RB1",
"gene_hgnc_id": 9884,
"hgvs_c": "c.411A>T",
"hgvs_p": "p.Glu137Asp",
"transcript": "ENST00000713856.1",
"protein_id": "ENSP00000519161.1",
"transcript_support_level": null,
"aa_start": 137,
"aa_end": null,
"aa_length": 851,
"cds_start": 411,
"cds_end": null,
"cds_length": 2556,
"cdna_start": 569,
"cdna_end": null,
"cdna_length": 4110,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RB1",
"gene_hgnc_id": 9884,
"hgvs_c": "c.411A>T",
"hgvs_p": "p.Glu137Asp",
"transcript": "NM_001407166.1",
"protein_id": "NP_001394095.1",
"transcript_support_level": null,
"aa_start": 137,
"aa_end": null,
"aa_length": 568,
"cds_start": 411,
"cds_end": null,
"cds_length": 1707,
"cdna_start": 573,
"cdna_end": null,
"cdna_length": 6581,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RB1",
"gene_hgnc_id": 9884,
"hgvs_c": "n.573A>T",
"hgvs_p": null,
"transcript": "ENST00000525036.1",
"protein_id": null,
"transcript_support_level": 3,
"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": 1490,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RB1",
"gene_hgnc_id": 9884,
"hgvs_c": "n.411A>T",
"hgvs_p": null,
"transcript": "ENST00000713859.1",
"protein_id": "ENSP00000519164.1",
"transcript_support_level": null,
"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": 4494,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "RB1",
"gene_hgnc_id": 9884,
"dbsnp": "rs3092902",
"frequency_reference_population": 0.0006839852,
"hom_count_reference_population": 1,
"allele_count_reference_population": 1103,
"gnomad_exomes_af": 0.000714871,
"gnomad_genomes_af": 0.000387638,
"gnomad_exomes_ac": 1044,
"gnomad_genomes_ac": 59,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.1684122383594513,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.604,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.122,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 2.548,
"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": -14,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Moderate,BP6_Very_Strong,BS2",
"acmg_by_gene": [
{
"score": -14,
"benign_score": 14,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6_Very_Strong",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000267163.6",
"gene_symbol": "RB1",
"hgnc_id": 9884,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.411A>T",
"hgvs_p": "p.Glu137Asp"
}
],
"clinvar_disease": "Bone osteosarcoma,Hereditary cancer-predisposing syndrome,Malignant tumor of urinary bladder,RB1-related disorder,Retinoblastoma,Small cell lung carcinoma,not provided,not specified",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:9 B:4",
"phenotype_combined": "not provided|Hereditary cancer-predisposing syndrome|RB1-related disorder|Malignant tumor of urinary bladder;Small cell lung carcinoma;Retinoblastoma;Bone osteosarcoma|not specified|Retinoblastoma",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}