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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: 3-39265765-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=39265765&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 12,
"criteria": [
"BP4_Strong",
"BA1"
],
"effects": [
"missense_variant"
],
"gene_symbol": "CX3CR1",
"hgnc_id": 2558,
"hgvs_c": "c.841G>A",
"hgvs_p": "p.Val281Ile",
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -12,
"transcript": "NM_001171174.1",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BA1",
"acmg_score": -12,
"allele_count_reference_population": 411519,
"alphamissense_prediction": null,
"alphamissense_score": 0.0754,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.61,
"chr": "3",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.0035637319087982178,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 355,
"aa_ref": "V",
"aa_start": 249,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3106,
"cdna_start": 837,
"cds_end": null,
"cds_length": 1068,
"cds_start": 745,
"consequences": [
"missense_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "NM_001337.4",
"gene_hgnc_id": 2558,
"gene_symbol": "CX3CR1",
"hgvs_c": "c.745G>A",
"hgvs_p": "p.Val249Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000399220.3",
"protein_coding": true,
"protein_id": "NP_001328.1",
"strand": false,
"transcript": "NM_001337.4",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 355,
"aa_ref": "V",
"aa_start": 249,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 3106,
"cdna_start": 837,
"cds_end": null,
"cds_length": 1068,
"cds_start": 745,
"consequences": [
"missense_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000399220.3",
"gene_hgnc_id": 2558,
"gene_symbol": "CX3CR1",
"hgvs_c": "c.745G>A",
"hgvs_p": "p.Val249Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001337.4",
"protein_coding": true,
"protein_id": "ENSP00000382166.3",
"strand": false,
"transcript": "ENST00000399220.3",
"transcript_support_level": 1
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 387,
"aa_ref": "V",
"aa_start": 281,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3152,
"cdna_start": 881,
"cds_end": null,
"cds_length": 1164,
"cds_start": 841,
"consequences": [
"missense_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "NM_001171174.1",
"gene_hgnc_id": 2558,
"gene_symbol": "CX3CR1",
"hgvs_c": "c.841G>A",
"hgvs_p": "p.Val281Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001164645.1",
"strand": false,
"transcript": "NM_001171174.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 387,
"aa_ref": "V",
"aa_start": 281,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3151,
"cdna_start": 881,
"cds_end": null,
"cds_length": 1164,
"cds_start": 841,
"consequences": [
"missense_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000358309.3",
"gene_hgnc_id": 2558,
"gene_symbol": "CX3CR1",
"hgvs_c": "c.841G>A",
"hgvs_p": "p.Val281Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000351059.3",
"strand": false,
"transcript": "ENST00000358309.3",
"transcript_support_level": 2
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 355,
"aa_ref": "V",
"aa_start": 249,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3254,
"cdna_start": 985,
"cds_end": null,
"cds_length": 1068,
"cds_start": 745,
"consequences": [
"missense_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "NM_001171171.2",
"gene_hgnc_id": 2558,
"gene_symbol": "CX3CR1",
"hgvs_c": "c.745G>A",
"hgvs_p": "p.Val249Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001164642.1",
"strand": false,
"transcript": "NM_001171171.2",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 355,
"aa_ref": "V",
"aa_start": 249,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3216,
"cdna_start": 947,
"cds_end": null,
"cds_length": 1068,
"cds_start": 745,
"consequences": [
"missense_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "NM_001171172.2",
"gene_hgnc_id": 2558,
"gene_symbol": "CX3CR1",
"hgvs_c": "c.745G>A",
"hgvs_p": "p.Val249Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001164643.1",
"strand": false,
"transcript": "NM_001171172.2",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 355,
"aa_ref": "V",
"aa_start": 249,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3255,
"cdna_start": 985,
"cds_end": null,
"cds_length": 1068,
"cds_start": 745,
"consequences": [
"missense_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000541347.5",
"gene_hgnc_id": 2558,
"gene_symbol": "CX3CR1",
"hgvs_c": "c.745G>A",
"hgvs_p": "p.Val249Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000439140.1",
"strand": false,
"transcript": "ENST00000541347.5",
"transcript_support_level": 4
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 355,
"aa_ref": "V",
"aa_start": 249,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3215,
"cdna_start": 945,
"cds_end": null,
"cds_length": 1068,
"cds_start": 745,
"consequences": [
"missense_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000542107.5",
"gene_hgnc_id": 2558,
"gene_symbol": "CX3CR1",
"hgvs_c": "c.745G>A",
"hgvs_p": "p.Val249Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000444928.1",
"strand": false,
"transcript": "ENST00000542107.5",
"transcript_support_level": 4
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 355,
"aa_ref": "V",
"aa_start": 249,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3296,
"cdna_start": 1029,
"cds_end": null,
"cds_length": 1068,
"cds_start": 745,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000864857.1",
"gene_hgnc_id": 2558,
"gene_symbol": "CX3CR1",
"hgvs_c": "c.745G>A",
"hgvs_p": "p.Val249Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000534916.1",
"strand": false,
"transcript": "ENST00000864857.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 355,
"aa_ref": "V",
"aa_start": 249,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3115,
"cdna_start": 846,
"cds_end": null,
"cds_length": 1068,
"cds_start": 745,
"consequences": [
"missense_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000864858.1",
"gene_hgnc_id": 2558,
"gene_symbol": "CX3CR1",
"hgvs_c": "c.745G>A",
"hgvs_p": "p.Val249Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000534917.1",
"strand": false,
"transcript": "ENST00000864858.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 355,
"aa_ref": "V",
"aa_start": 249,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3383,
"cdna_start": 1115,
"cds_end": null,
"cds_length": 1068,
"cds_start": 745,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000864859.1",
"gene_hgnc_id": 2558,
"gene_symbol": "CX3CR1",
"hgvs_c": "c.745G>A",
"hgvs_p": "p.Val249Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000534918.1",
"strand": false,
"transcript": "ENST00000864859.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 355,
"aa_ref": "V",
"aa_start": 249,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3292,
"cdna_start": 1024,
"cds_end": null,
"cds_length": 1068,
"cds_start": 745,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000963325.1",
"gene_hgnc_id": 2558,
"gene_symbol": "CX3CR1",
"hgvs_c": "c.745G>A",
"hgvs_p": "p.Val249Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000633384.1",
"strand": false,
"transcript": "ENST00000963325.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 355,
"aa_ref": "V",
"aa_start": 249,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3200,
"cdna_start": 929,
"cds_end": null,
"cds_length": 1068,
"cds_start": 745,
"consequences": [
"missense_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "XM_047447538.1",
"gene_hgnc_id": 2558,
"gene_symbol": "CX3CR1",
"hgvs_c": "c.745G>A",
"hgvs_p": "p.Val249Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047303494.1",
"strand": false,
"transcript": "XM_047447538.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 165,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 699,
"cdna_start": null,
"cds_end": null,
"cds_length": 499,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000435290.1",
"gene_hgnc_id": 2558,
"gene_symbol": "CX3CR1",
"hgvs_c": "c.*246G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000394960.1",
"strand": true,
"transcript": "ENST00000435290.1",
"transcript_support_level": 4
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs3732379",
"effect": "missense_variant",
"frequency_reference_population": 0.25503698,
"gene_hgnc_id": 2558,
"gene_symbol": "CX3CR1",
"gnomad_exomes_ac": 378032,
"gnomad_exomes_af": 0.258651,
"gnomad_exomes_homalt": 51275,
"gnomad_genomes_ac": 33487,
"gnomad_genomes_af": 0.220289,
"gnomad_genomes_homalt": 4122,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 55397,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": null,
"phenotype_combined": null,
"phylop100way_prediction": "Benign",
"phylop100way_score": -1.966,
"pos": 39265765,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.046,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_001171174.1"
}
]
}