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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: 3-39265853-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=39265853&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 39265853,
"ref": "A",
"alt": "G",
"effect": "synonymous_variant",
"transcript": "NM_001171174.1",
"consequences": [
{
"aa_ref": "F",
"aa_alt": "F",
"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": "CX3CR1",
"gene_hgnc_id": 2558,
"hgvs_c": "c.657T>C",
"hgvs_p": "p.Phe219Phe",
"transcript": "NM_001337.4",
"protein_id": "NP_001328.1",
"transcript_support_level": null,
"aa_start": 219,
"aa_end": null,
"aa_length": 355,
"cds_start": 657,
"cds_end": null,
"cds_length": 1068,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000399220.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001337.4"
},
{
"aa_ref": "F",
"aa_alt": "F",
"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": "CX3CR1",
"gene_hgnc_id": 2558,
"hgvs_c": "c.657T>C",
"hgvs_p": "p.Phe219Phe",
"transcript": "ENST00000399220.3",
"protein_id": "ENSP00000382166.3",
"transcript_support_level": 1,
"aa_start": 219,
"aa_end": null,
"aa_length": 355,
"cds_start": 657,
"cds_end": null,
"cds_length": 1068,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001337.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000399220.3"
},
{
"aa_ref": "F",
"aa_alt": "F",
"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": "CX3CR1",
"gene_hgnc_id": 2558,
"hgvs_c": "c.753T>C",
"hgvs_p": "p.Phe251Phe",
"transcript": "NM_001171174.1",
"protein_id": "NP_001164645.1",
"transcript_support_level": null,
"aa_start": 251,
"aa_end": null,
"aa_length": 387,
"cds_start": 753,
"cds_end": null,
"cds_length": 1164,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001171174.1"
},
{
"aa_ref": "F",
"aa_alt": "F",
"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": "CX3CR1",
"gene_hgnc_id": 2558,
"hgvs_c": "c.753T>C",
"hgvs_p": "p.Phe251Phe",
"transcript": "ENST00000358309.3",
"protein_id": "ENSP00000351059.3",
"transcript_support_level": 2,
"aa_start": 251,
"aa_end": null,
"aa_length": 387,
"cds_start": 753,
"cds_end": null,
"cds_length": 1164,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000358309.3"
},
{
"aa_ref": "F",
"aa_alt": "F",
"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": "CX3CR1",
"gene_hgnc_id": 2558,
"hgvs_c": "c.657T>C",
"hgvs_p": "p.Phe219Phe",
"transcript": "NM_001171171.2",
"protein_id": "NP_001164642.1",
"transcript_support_level": null,
"aa_start": 219,
"aa_end": null,
"aa_length": 355,
"cds_start": 657,
"cds_end": null,
"cds_length": 1068,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001171171.2"
},
{
"aa_ref": "F",
"aa_alt": "F",
"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": "CX3CR1",
"gene_hgnc_id": 2558,
"hgvs_c": "c.657T>C",
"hgvs_p": "p.Phe219Phe",
"transcript": "NM_001171172.2",
"protein_id": "NP_001164643.1",
"transcript_support_level": null,
"aa_start": 219,
"aa_end": null,
"aa_length": 355,
"cds_start": 657,
"cds_end": null,
"cds_length": 1068,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001171172.2"
},
{
"aa_ref": "F",
"aa_alt": "F",
"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": "CX3CR1",
"gene_hgnc_id": 2558,
"hgvs_c": "c.657T>C",
"hgvs_p": "p.Phe219Phe",
"transcript": "ENST00000541347.5",
"protein_id": "ENSP00000439140.1",
"transcript_support_level": 4,
"aa_start": 219,
"aa_end": null,
"aa_length": 355,
"cds_start": 657,
"cds_end": null,
"cds_length": 1068,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000541347.5"
},
{
"aa_ref": "F",
"aa_alt": "F",
"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": "CX3CR1",
"gene_hgnc_id": 2558,
"hgvs_c": "c.657T>C",
"hgvs_p": "p.Phe219Phe",
"transcript": "ENST00000542107.5",
"protein_id": "ENSP00000444928.1",
"transcript_support_level": 4,
"aa_start": 219,
"aa_end": null,
"aa_length": 355,
"cds_start": 657,
"cds_end": null,
"cds_length": 1068,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000542107.5"
},
{
"aa_ref": "F",
"aa_alt": "F",
"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": "CX3CR1",
"gene_hgnc_id": 2558,
"hgvs_c": "c.657T>C",
"hgvs_p": "p.Phe219Phe",
"transcript": "ENST00000864857.1",
"protein_id": "ENSP00000534916.1",
"transcript_support_level": null,
"aa_start": 219,
"aa_end": null,
"aa_length": 355,
"cds_start": 657,
"cds_end": null,
"cds_length": 1068,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000864857.1"
},
{
"aa_ref": "F",
"aa_alt": "F",
"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": "CX3CR1",
"gene_hgnc_id": 2558,
"hgvs_c": "c.657T>C",
"hgvs_p": "p.Phe219Phe",
"transcript": "ENST00000864858.1",
"protein_id": "ENSP00000534917.1",
"transcript_support_level": null,
"aa_start": 219,
"aa_end": null,
"aa_length": 355,
"cds_start": 657,
"cds_end": null,
"cds_length": 1068,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000864858.1"
},
{
"aa_ref": "F",
"aa_alt": "F",
"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": "CX3CR1",
"gene_hgnc_id": 2558,
"hgvs_c": "c.657T>C",
"hgvs_p": "p.Phe219Phe",
"transcript": "ENST00000864859.1",
"protein_id": "ENSP00000534918.1",
"transcript_support_level": null,
"aa_start": 219,
"aa_end": null,
"aa_length": 355,
"cds_start": 657,
"cds_end": null,
"cds_length": 1068,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000864859.1"
},
{
"aa_ref": "F",
"aa_alt": "F",
"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": "CX3CR1",
"gene_hgnc_id": 2558,
"hgvs_c": "c.657T>C",
"hgvs_p": "p.Phe219Phe",
"transcript": "ENST00000963325.1",
"protein_id": "ENSP00000633384.1",
"transcript_support_level": null,
"aa_start": 219,
"aa_end": null,
"aa_length": 355,
"cds_start": 657,
"cds_end": null,
"cds_length": 1068,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000963325.1"
},
{
"aa_ref": "F",
"aa_alt": "F",
"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": "CX3CR1",
"gene_hgnc_id": 2558,
"hgvs_c": "c.657T>C",
"hgvs_p": "p.Phe219Phe",
"transcript": "XM_047447538.1",
"protein_id": "XP_047303494.1",
"transcript_support_level": null,
"aa_start": 219,
"aa_end": null,
"aa_length": 355,
"cds_start": 657,
"cds_end": null,
"cds_length": 1068,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047447538.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CX3CR1",
"gene_hgnc_id": 2558,
"hgvs_c": "c.*158T>C",
"hgvs_p": null,
"transcript": "ENST00000435290.1",
"protein_id": "ENSP00000394960.1",
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": 165,
"cds_start": null,
"cds_end": null,
"cds_length": 499,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000435290.1"
}
],
"gene_symbol": "CX3CR1",
"gene_hgnc_id": 2558,
"dbsnp": "rs4986872",
"frequency_reference_population": 0.00012389763,
"hom_count_reference_population": 0,
"allele_count_reference_population": 200,
"gnomad_exomes_af": 0.0000574599,
"gnomad_genomes_af": 0.000761425,
"gnomad_exomes_ac": 84,
"gnomad_genomes_ac": 116,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.8500000238418579,
"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": -0.85,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -1.751,
"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": -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_001171174.1",
"gene_symbol": "CX3CR1",
"hgnc_id": 2558,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.753T>C",
"hgvs_p": "p.Phe251Phe"
}
],
"clinvar_disease": "CX3CR1-related disorder",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "CX3CR1-related disorder",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}