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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: 3-46373452-TACAGTCAGTATCAATTCTGGAAGAATTTCCAG-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=46373452&ref=TACAGTCAGTATCAATTCTGGAAGAATTTCCAG&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 46373452,
"ref": "TACAGTCAGTATCAATTCTGGAAGAATTTCCAG",
"alt": "T",
"effect": "frameshift_variant",
"transcript": "ENST00000292303.5",
"consequences": [
{
"aa_ref": "SQYQFWKNFQT",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CCR5",
"gene_hgnc_id": 1606,
"hgvs_c": "c.554_585delGTCAGTATCAATTCTGGAAGAATTTCCAGACA",
"hgvs_p": "p.Ser185fs",
"transcript": "NM_001394783.1",
"protein_id": "NP_001381712.1",
"transcript_support_level": null,
"aa_start": 185,
"aa_end": null,
"aa_length": 352,
"cds_start": 554,
"cds_end": null,
"cds_length": 1059,
"cdna_start": 608,
"cdna_end": null,
"cdna_length": 3358,
"mane_select": "ENST00000292303.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "SQYQFWKNFQT",
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CCR5",
"gene_hgnc_id": 1606,
"hgvs_c": "c.554_585delGTCAGTATCAATTCTGGAAGAATTTCCAGACA",
"hgvs_p": "p.Ser185fs",
"transcript": "ENST00000292303.5",
"protein_id": "ENSP00000292303.4",
"transcript_support_level": 1,
"aa_start": 185,
"aa_end": null,
"aa_length": 352,
"cds_start": 554,
"cds_end": null,
"cds_length": 1059,
"cdna_start": 608,
"cdna_end": null,
"cdna_length": 3358,
"mane_select": "NM_001394783.1",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "SQYQFWKNFQT",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CCR5",
"gene_hgnc_id": 1606,
"hgvs_c": "c.554_585delGTCAGTATCAATTCTGGAAGAATTTCCAGACA",
"hgvs_p": "p.Ser185fs",
"transcript": "NM_000579.4",
"protein_id": "NP_000570.1",
"transcript_support_level": null,
"aa_start": 185,
"aa_end": null,
"aa_length": 352,
"cds_start": 554,
"cds_end": null,
"cds_length": 1059,
"cdna_start": 911,
"cdna_end": null,
"cdna_length": 3661,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "SQYQFWKNFQT",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CCR5",
"gene_hgnc_id": 1606,
"hgvs_c": "c.554_585delGTCAGTATCAATTCTGGAAGAATTTCCAGACA",
"hgvs_p": "p.Ser185fs",
"transcript": "NM_001100168.2",
"protein_id": "NP_001093638.1",
"transcript_support_level": null,
"aa_start": 185,
"aa_end": null,
"aa_length": 352,
"cds_start": 554,
"cds_end": null,
"cds_length": 1059,
"cdna_start": 676,
"cdna_end": null,
"cdna_length": 3426,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "SQYQFWKNFQT",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CCR5",
"gene_hgnc_id": 1606,
"hgvs_c": "c.554_585delGTCAGTATCAATTCTGGAAGAATTTCCAGACA",
"hgvs_p": "p.Ser185fs",
"transcript": "ENST00000445772.1",
"protein_id": "ENSP00000404881.1",
"transcript_support_level": 6,
"aa_start": 185,
"aa_end": null,
"aa_length": 352,
"cds_start": 554,
"cds_end": null,
"cds_length": 1059,
"cdna_start": 787,
"cdna_end": null,
"cdna_length": 1292,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CCR5AS",
"gene_hgnc_id": 54398,
"hgvs_c": "n.450_481delCTGGAAATTCTTCCAGAATTGATACTGACTGT",
"hgvs_p": null,
"transcript": "ENST00000717851.1",
"protein_id": null,
"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": 1075,
"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": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "CCR5AS",
"gene_hgnc_id": 54398,
"hgvs_c": "n.399-2067_399-2036delCTGGAAATTCTTCCAGAATTGATACTGACTGT",
"hgvs_p": null,
"transcript": "ENST00000451485.3",
"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": 1634,
"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": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "CCR5AS",
"gene_hgnc_id": 54398,
"hgvs_c": "n.289-2067_289-2036delCTGGAAATTCTTCCAGAATTGATACTGACTGT",
"hgvs_p": null,
"transcript": "ENST00000701879.2",
"protein_id": null,
"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": 1117,
"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": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "CCR5AS",
"gene_hgnc_id": 54398,
"hgvs_c": "n.151-2067_151-2036delCTGGAAATTCTTCCAGAATTGATACTGACTGT",
"hgvs_p": null,
"transcript": "ENST00000717843.1",
"protein_id": null,
"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": 748,
"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": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "CCR5AS",
"gene_hgnc_id": 54398,
"hgvs_c": "n.399-2067_399-2036delCTGGAAATTCTTCCAGAATTGATACTGACTGT",
"hgvs_p": null,
"transcript": "NR_125406.2",
"protein_id": null,
"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": 1634,
"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": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "CCR5AS",
"gene_hgnc_id": 54398,
"hgvs_c": "n.171-2067_171-2036delCTGGAAATTCTTCCAGAATTGATACTGACTGT",
"hgvs_p": null,
"transcript": "NR_185891.1",
"protein_id": null,
"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": 1406,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "CCR5",
"gene_hgnc_id": 1606,
"dbsnp": "rs333",
"frequency_reference_population": 0.09773092,
"hom_count_reference_population": 8868,
"allele_count_reference_population": 157725,
"gnomad_exomes_af": 0.100437,
"gnomad_genomes_af": 0.0717309,
"gnomad_exomes_ac": 146811,
"gnomad_genomes_ac": 10914,
"gnomad_exomes_homalt": 8315,
"gnomad_genomes_homalt": 553,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"splice_score_selected": null,
"splice_prediction_selected": null,
"splice_source_selected": null,
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 0.894,
"phylop100way_prediction": "Benign",
"spliceai_max_score": null,
"spliceai_max_prediction": null,
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -10,
"acmg_classification": "Benign",
"acmg_criteria": "BP6_Moderate,BA1",
"acmg_by_gene": [
{
"score": -10,
"benign_score": 10,
"pathogenic_score": 0,
"criteria": [
"BP6_Moderate",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000292303.5",
"gene_symbol": "CCR5",
"hgnc_id": 1606,
"effects": [
"frameshift_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.554_585delGTCAGTATCAATTCTGGAAGAATTTCCAGACA",
"hgvs_p": "p.Ser185fs"
},
{
"score": -10,
"benign_score": 10,
"pathogenic_score": 0,
"criteria": [
"BP6_Moderate",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000717851.1",
"gene_symbol": "CCR5AS",
"hgnc_id": 54398,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.450_481delCTGGAAATTCTTCCAGAATTGATACTGACTGT",
"hgvs_p": null
}
],
"clinvar_disease": " susceptibility to,CCR5-related disorder,Multiple sclerosis modifier of disease progression,Resistance to hepatitis C virus,Susceptibility to HIV infection,West Nile virus,not provided",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "B:1",
"phenotype_combined": "Multiple sclerosis modifier of disease progression|Susceptibility to HIV infection|Resistance to hepatitis C virus|West Nile virus, susceptibility to|not provided|CCR5-related disorder",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}