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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: 5-150055267-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=150055267&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 150055267,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_005211.4",
"consequences": [
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSF1R",
"gene_hgnc_id": 2433,
"hgvs_c": "c.2624T>C",
"hgvs_p": "p.Met875Thr",
"transcript": "NM_001288705.3",
"protein_id": "NP_001275634.1",
"transcript_support_level": null,
"aa_start": 875,
"aa_end": null,
"aa_length": 972,
"cds_start": 2624,
"cds_end": null,
"cds_length": 2919,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000675795.1",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001288705.3"
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSF1R",
"gene_hgnc_id": 2433,
"hgvs_c": "c.2624T>C",
"hgvs_p": "p.Met875Thr",
"transcript": "ENST00000675795.1",
"protein_id": "ENSP00000501699.1",
"transcript_support_level": null,
"aa_start": 875,
"aa_end": null,
"aa_length": 972,
"cds_start": 2624,
"cds_end": null,
"cds_length": 2919,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001288705.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000675795.1"
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSF1R",
"gene_hgnc_id": 2433,
"hgvs_c": "c.2624T>C",
"hgvs_p": "p.Met875Thr",
"transcript": "ENST00000286301.7",
"protein_id": "ENSP00000286301.3",
"transcript_support_level": 1,
"aa_start": 875,
"aa_end": null,
"aa_length": 972,
"cds_start": 2624,
"cds_end": null,
"cds_length": 2919,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000286301.7"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSF1R",
"gene_hgnc_id": 2433,
"hgvs_c": "n.*445T>C",
"hgvs_p": null,
"transcript": "ENST00000504875.5",
"protein_id": "ENSP00000422212.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000504875.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSF1R",
"gene_hgnc_id": 2433,
"hgvs_c": "n.*445T>C",
"hgvs_p": null,
"transcript": "ENST00000504875.5",
"protein_id": "ENSP00000422212.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000504875.5"
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSF1R",
"gene_hgnc_id": 2433,
"hgvs_c": "c.2699T>C",
"hgvs_p": "p.Met900Thr",
"transcript": "ENST00000960687.1",
"protein_id": "ENSP00000630746.1",
"transcript_support_level": null,
"aa_start": 900,
"aa_end": null,
"aa_length": 997,
"cds_start": 2699,
"cds_end": null,
"cds_length": 2994,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000960687.1"
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSF1R",
"gene_hgnc_id": 2433,
"hgvs_c": "c.2624T>C",
"hgvs_p": "p.Met875Thr",
"transcript": "NM_001349736.2",
"protein_id": "NP_001336665.1",
"transcript_support_level": null,
"aa_start": 875,
"aa_end": null,
"aa_length": 972,
"cds_start": 2624,
"cds_end": null,
"cds_length": 2919,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001349736.2"
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSF1R",
"gene_hgnc_id": 2433,
"hgvs_c": "c.2624T>C",
"hgvs_p": "p.Met875Thr",
"transcript": "NM_001375320.1",
"protein_id": "NP_001362249.1",
"transcript_support_level": null,
"aa_start": 875,
"aa_end": null,
"aa_length": 972,
"cds_start": 2624,
"cds_end": null,
"cds_length": 2919,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001375320.1"
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSF1R",
"gene_hgnc_id": 2433,
"hgvs_c": "c.2624T>C",
"hgvs_p": "p.Met875Thr",
"transcript": "NM_005211.4",
"protein_id": "NP_005202.2",
"transcript_support_level": null,
"aa_start": 875,
"aa_end": null,
"aa_length": 972,
"cds_start": 2624,
"cds_end": null,
"cds_length": 2919,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_005211.4"
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSF1R",
"gene_hgnc_id": 2433,
"hgvs_c": "c.2621T>C",
"hgvs_p": "p.Met874Thr",
"transcript": "ENST00000911112.1",
"protein_id": "ENSP00000581171.1",
"transcript_support_level": null,
"aa_start": 874,
"aa_end": null,
"aa_length": 971,
"cds_start": 2621,
"cds_end": null,
"cds_length": 2916,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000911112.1"
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSF1R",
"gene_hgnc_id": 2433,
"hgvs_c": "c.2624T>C",
"hgvs_p": "p.Met875Thr",
"transcript": "ENST00000911110.1",
"protein_id": "ENSP00000581169.1",
"transcript_support_level": null,
"aa_start": 875,
"aa_end": null,
"aa_length": 970,
"cds_start": 2624,
"cds_end": null,
"cds_length": 2913,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000911110.1"
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSF1R",
"gene_hgnc_id": 2433,
"hgvs_c": "c.2618T>C",
"hgvs_p": "p.Met873Thr",
"transcript": "ENST00000960688.1",
"protein_id": "ENSP00000630747.1",
"transcript_support_level": null,
"aa_start": 873,
"aa_end": null,
"aa_length": 970,
"cds_start": 2618,
"cds_end": null,
"cds_length": 2913,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000960688.1"
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSF1R",
"gene_hgnc_id": 2433,
"hgvs_c": "c.2585T>C",
"hgvs_p": "p.Met862Thr",
"transcript": "ENST00000911114.1",
"protein_id": "ENSP00000581173.1",
"transcript_support_level": null,
"aa_start": 862,
"aa_end": null,
"aa_length": 959,
"cds_start": 2585,
"cds_end": null,
"cds_length": 2880,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000911114.1"
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSF1R",
"gene_hgnc_id": 2433,
"hgvs_c": "c.2519T>C",
"hgvs_p": "p.Met840Thr",
"transcript": "ENST00000911115.1",
"protein_id": "ENSP00000581174.1",
"transcript_support_level": null,
"aa_start": 840,
"aa_end": null,
"aa_length": 937,
"cds_start": 2519,
"cds_end": null,
"cds_length": 2814,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000911115.1"
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSF1R",
"gene_hgnc_id": 2433,
"hgvs_c": "c.2339T>C",
"hgvs_p": "p.Met780Thr",
"transcript": "ENST00000911111.1",
"protein_id": "ENSP00000581170.1",
"transcript_support_level": null,
"aa_start": 780,
"aa_end": null,
"aa_length": 877,
"cds_start": 2339,
"cds_end": null,
"cds_length": 2634,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000911111.1"
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSF1R",
"gene_hgnc_id": 2433,
"hgvs_c": "c.2180T>C",
"hgvs_p": "p.Met727Thr",
"transcript": "NM_001375321.1",
"protein_id": "NP_001362250.1",
"transcript_support_level": null,
"aa_start": 727,
"aa_end": null,
"aa_length": 824,
"cds_start": 2180,
"cds_end": null,
"cds_length": 2475,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001375321.1"
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSF1R",
"gene_hgnc_id": 2433,
"hgvs_c": "c.1919T>C",
"hgvs_p": "p.Met640Thr",
"transcript": "ENST00000911116.1",
"protein_id": "ENSP00000581175.1",
"transcript_support_level": null,
"aa_start": 640,
"aa_end": null,
"aa_length": 737,
"cds_start": 1919,
"cds_end": null,
"cds_length": 2214,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000911116.1"
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSF1R",
"gene_hgnc_id": 2433,
"hgvs_c": "c.1784T>C",
"hgvs_p": "p.Met595Thr",
"transcript": "ENST00000911113.1",
"protein_id": "ENSP00000581172.1",
"transcript_support_level": null,
"aa_start": 595,
"aa_end": null,
"aa_length": 692,
"cds_start": 1784,
"cds_end": null,
"cds_length": 2079,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000911113.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSF1R",
"gene_hgnc_id": 2433,
"hgvs_c": "n.2588T>C",
"hgvs_p": null,
"transcript": "NR_109969.2",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_109969.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSF1R",
"gene_hgnc_id": 2433,
"hgvs_c": "n.2517T>C",
"hgvs_p": null,
"transcript": "NR_164679.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_164679.1"
}
],
"gene_symbol": "CSF1R",
"gene_hgnc_id": 2433,
"dbsnp": "rs281860279",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9918431639671326,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.916,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9969,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.31,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 9.322,
"phylop100way_prediction": "Pathogenic",
"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": 8,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PP3_Strong,PP5_Moderate",
"acmg_by_gene": [
{
"score": 8,
"benign_score": 0,
"pathogenic_score": 8,
"criteria": [
"PM2",
"PP3_Strong",
"PP5_Moderate"
],
"verdict": "Likely_pathogenic",
"transcript": "NM_005211.4",
"gene_symbol": "CSF1R",
"hgnc_id": 2433,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.2624T>C",
"hgvs_p": "p.Met875Thr"
}
],
"clinvar_disease": "Hereditary diffuse leukoencephalopathy with spheroids,not provided",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "P:1",
"phenotype_combined": "Hereditary diffuse leukoencephalopathy with spheroids|not provided",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}