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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: 8-16168568-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=8&pos=16168568&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "8",
"pos": 16168568,
"ref": "C",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000262101.10",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSR1",
"gene_hgnc_id": 7376,
"hgvs_c": "c.520G>T",
"hgvs_p": "p.Asp174Tyr",
"transcript": "NM_138715.3",
"protein_id": "NP_619729.1",
"transcript_support_level": null,
"aa_start": 174,
"aa_end": null,
"aa_length": 451,
"cds_start": 520,
"cds_end": null,
"cds_length": 1356,
"cdna_start": 578,
"cdna_end": null,
"cdna_length": 3618,
"mane_select": "ENST00000262101.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSR1",
"gene_hgnc_id": 7376,
"hgvs_c": "c.520G>T",
"hgvs_p": "p.Asp174Tyr",
"transcript": "ENST00000262101.10",
"protein_id": "ENSP00000262101.5",
"transcript_support_level": 1,
"aa_start": 174,
"aa_end": null,
"aa_length": 451,
"cds_start": 520,
"cds_end": null,
"cds_length": 1356,
"cdna_start": 578,
"cdna_end": null,
"cdna_length": 3618,
"mane_select": "NM_138715.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSR1",
"gene_hgnc_id": 7376,
"hgvs_c": "c.574G>T",
"hgvs_p": "p.Asp192Tyr",
"transcript": "ENST00000445506.6",
"protein_id": "ENSP00000405453.2",
"transcript_support_level": 1,
"aa_start": 192,
"aa_end": null,
"aa_length": 469,
"cds_start": 574,
"cds_end": null,
"cds_length": 1410,
"cdna_start": 638,
"cdna_end": null,
"cdna_length": 1513,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSR1",
"gene_hgnc_id": 7376,
"hgvs_c": "c.520G>T",
"hgvs_p": "p.Asp174Tyr",
"transcript": "ENST00000355282.6",
"protein_id": "ENSP00000347430.2",
"transcript_support_level": 1,
"aa_start": 174,
"aa_end": null,
"aa_length": 388,
"cds_start": 520,
"cds_end": null,
"cds_length": 1167,
"cdna_start": 520,
"cdna_end": null,
"cdna_length": 1167,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSR1",
"gene_hgnc_id": 7376,
"hgvs_c": "c.520G>T",
"hgvs_p": "p.Asp174Tyr",
"transcript": "ENST00000381998.8",
"protein_id": "ENSP00000371428.4",
"transcript_support_level": 1,
"aa_start": 174,
"aa_end": null,
"aa_length": 358,
"cds_start": 520,
"cds_end": null,
"cds_length": 1077,
"cdna_start": 586,
"cdna_end": null,
"cdna_length": 2826,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSR1",
"gene_hgnc_id": 7376,
"hgvs_c": "c.574G>T",
"hgvs_p": "p.Asp192Tyr",
"transcript": "NM_001363744.1",
"protein_id": "NP_001350673.1",
"transcript_support_level": null,
"aa_start": 192,
"aa_end": null,
"aa_length": 469,
"cds_start": 574,
"cds_end": null,
"cds_length": 1410,
"cdna_start": 638,
"cdna_end": null,
"cdna_length": 3678,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSR1",
"gene_hgnc_id": 7376,
"hgvs_c": "c.520G>T",
"hgvs_p": "p.Asp174Tyr",
"transcript": "NM_138716.3",
"protein_id": "NP_619730.1",
"transcript_support_level": null,
"aa_start": 174,
"aa_end": null,
"aa_length": 388,
"cds_start": 520,
"cds_end": null,
"cds_length": 1167,
"cdna_start": 578,
"cdna_end": null,
"cdna_length": 3429,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSR1",
"gene_hgnc_id": 7376,
"hgvs_c": "c.520G>T",
"hgvs_p": "p.Asp174Tyr",
"transcript": "ENST00000350896.3",
"protein_id": "ENSP00000262100.3",
"transcript_support_level": 5,
"aa_start": 174,
"aa_end": null,
"aa_length": 388,
"cds_start": 520,
"cds_end": null,
"cds_length": 1167,
"cdna_start": 718,
"cdna_end": null,
"cdna_length": 3572,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSR1",
"gene_hgnc_id": 7376,
"hgvs_c": "c.520G>T",
"hgvs_p": "p.Asp174Tyr",
"transcript": "NM_002445.4",
"protein_id": "NP_002436.1",
"transcript_support_level": null,
"aa_start": 174,
"aa_end": null,
"aa_length": 358,
"cds_start": 520,
"cds_end": null,
"cds_length": 1077,
"cdna_start": 578,
"cdna_end": null,
"cdna_length": 2820,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSR1",
"gene_hgnc_id": 7376,
"hgvs_c": "c.574G>T",
"hgvs_p": "p.Asp192Tyr",
"transcript": "XM_024447161.2",
"protein_id": "XP_024302929.1",
"transcript_support_level": null,
"aa_start": 192,
"aa_end": null,
"aa_length": 376,
"cds_start": 574,
"cds_end": null,
"cds_length": 1131,
"cdna_start": 638,
"cdna_end": null,
"cdna_length": 2880,
"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": 7,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "MSR1",
"gene_hgnc_id": 7376,
"hgvs_c": "n.104-4317G>T",
"hgvs_p": null,
"transcript": "ENST00000519060.6",
"protein_id": "ENSP00000428865.1",
"transcript_support_level": 5,
"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": 1009,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "MSR1",
"gene_hgnc_id": 7376,
"dbsnp": "rs72552387",
"frequency_reference_population": 0.0012142825,
"hom_count_reference_population": 26,
"allele_count_reference_population": 1960,
"gnomad_exomes_af": 0.000691603,
"gnomad_genomes_af": 0.00623112,
"gnomad_exomes_ac": 1011,
"gnomad_genomes_ac": 949,
"gnomad_exomes_homalt": 16,
"gnomad_genomes_homalt": 10,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.07389017939567566,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.507,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.2873,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.05,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 1.113,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.02,
"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": -7,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Moderate,BS1_Supporting,BS2",
"acmg_by_gene": [
{
"score": -7,
"benign_score": 7,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BS1_Supporting",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000262101.10",
"gene_symbol": "MSR1",
"hgnc_id": 7376,
"effects": [
"missense_variant"
],
"inheritance_mode": "Unknown",
"hgvs_c": "c.520G>T",
"hgvs_p": "p.Asp174Tyr"
}
],
"clinvar_disease": "Prostate cancer,not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:2",
"phenotype_combined": "Prostate cancer|not provided",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}