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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: 12-106696423-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=106696423&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 106696423,
"ref": "T",
"alt": "C",
"effect": "synonymous_variant",
"transcript": "ENST00000392842.6",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFX4",
"gene_hgnc_id": 9985,
"hgvs_c": "c.810T>C",
"hgvs_p": "p.Thr270Thr",
"transcript": "NM_213594.3",
"protein_id": "NP_998759.1",
"transcript_support_level": null,
"aa_start": 270,
"aa_end": null,
"aa_length": 735,
"cds_start": 810,
"cds_end": null,
"cds_length": 2208,
"cdna_start": 1127,
"cdna_end": null,
"cdna_length": 3859,
"mane_select": "ENST00000392842.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFX4",
"gene_hgnc_id": 9985,
"hgvs_c": "c.810T>C",
"hgvs_p": "p.Thr270Thr",
"transcript": "ENST00000392842.6",
"protein_id": "ENSP00000376585.1",
"transcript_support_level": 1,
"aa_start": 270,
"aa_end": null,
"aa_length": 735,
"cds_start": 810,
"cds_end": null,
"cds_length": 2208,
"cdna_start": 1127,
"cdna_end": null,
"cdna_length": 3859,
"mane_select": "NM_213594.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFX4",
"gene_hgnc_id": 9985,
"hgvs_c": "c.837T>C",
"hgvs_p": "p.Thr279Thr",
"transcript": "ENST00000357881.8",
"protein_id": "ENSP00000350552.4",
"transcript_support_level": 1,
"aa_start": 279,
"aa_end": null,
"aa_length": 744,
"cds_start": 837,
"cds_end": null,
"cds_length": 2235,
"cdna_start": 977,
"cdna_end": null,
"cdna_length": 2565,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFX4",
"gene_hgnc_id": 9985,
"hgvs_c": "c.528T>C",
"hgvs_p": "p.Thr176Thr",
"transcript": "ENST00000229387.6",
"protein_id": "ENSP00000229387.5",
"transcript_support_level": 1,
"aa_start": 176,
"aa_end": null,
"aa_length": 641,
"cds_start": 528,
"cds_end": null,
"cds_length": 1926,
"cdna_start": 646,
"cdna_end": null,
"cdna_length": 3378,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFX4",
"gene_hgnc_id": 9985,
"hgvs_c": "n.942T>C",
"hgvs_p": null,
"transcript": "ENST00000536688.5",
"protein_id": null,
"transcript_support_level": 1,
"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": 2186,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFX4",
"gene_hgnc_id": 9985,
"hgvs_c": "c.837T>C",
"hgvs_p": "p.Thr279Thr",
"transcript": "NM_001206691.2",
"protein_id": "NP_001193620.1",
"transcript_support_level": null,
"aa_start": 279,
"aa_end": null,
"aa_length": 744,
"cds_start": 837,
"cds_end": null,
"cds_length": 2235,
"cdna_start": 966,
"cdna_end": null,
"cdna_length": 3698,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFX4",
"gene_hgnc_id": 9985,
"hgvs_c": "c.528T>C",
"hgvs_p": "p.Thr176Thr",
"transcript": "NM_032491.6",
"protein_id": "NP_115880.2",
"transcript_support_level": null,
"aa_start": 176,
"aa_end": null,
"aa_length": 641,
"cds_start": 528,
"cds_end": null,
"cds_length": 1926,
"cdna_start": 613,
"cdna_end": null,
"cdna_length": 3345,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFX4",
"gene_hgnc_id": 9985,
"hgvs_c": "c.645T>C",
"hgvs_p": "p.Thr215Thr",
"transcript": "ENST00000551640.5",
"protein_id": "ENSP00000448694.1",
"transcript_support_level": 5,
"aa_start": 215,
"aa_end": null,
"aa_length": 255,
"cds_start": 645,
"cds_end": null,
"cds_length": 769,
"cdna_start": 674,
"cdna_end": null,
"cdna_length": 798,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFX4",
"gene_hgnc_id": 9985,
"hgvs_c": "c.108T>C",
"hgvs_p": "p.Thr36Thr",
"transcript": "ENST00000539967.6",
"protein_id": "ENSP00000473326.1",
"transcript_support_level": 5,
"aa_start": 36,
"aa_end": null,
"aa_length": 144,
"cds_start": 108,
"cds_end": null,
"cds_length": 436,
"cdna_start": 725,
"cdna_end": null,
"cdna_length": 1053,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFX4",
"gene_hgnc_id": 9985,
"hgvs_c": "n.*62T>C",
"hgvs_p": null,
"transcript": "ENST00000536722.5",
"protein_id": "ENSP00000444163.1",
"transcript_support_level": 2,
"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": 1228,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFX4",
"gene_hgnc_id": 9985,
"hgvs_c": "n.*385T>C",
"hgvs_p": null,
"transcript": "ENST00000552917.1",
"protein_id": "ENSP00000449732.1",
"transcript_support_level": 4,
"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": 594,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFX4",
"gene_hgnc_id": 9985,
"hgvs_c": "n.*62T>C",
"hgvs_p": null,
"transcript": "ENST00000536722.5",
"protein_id": "ENSP00000444163.1",
"transcript_support_level": 2,
"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": 1228,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFX4",
"gene_hgnc_id": 9985,
"hgvs_c": "n.*385T>C",
"hgvs_p": null,
"transcript": "ENST00000552917.1",
"protein_id": "ENSP00000449732.1",
"transcript_support_level": 4,
"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": 594,
"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": "ENSG00000257545",
"gene_hgnc_id": null,
"hgvs_c": "n.142+78267A>G",
"hgvs_p": null,
"transcript": "ENST00000549203.2",
"protein_id": null,
"transcript_support_level": 4,
"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": 569,
"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": "ENSG00000257545",
"gene_hgnc_id": null,
"hgvs_c": "n.229+78267A>G",
"hgvs_p": null,
"transcript": "ENST00000551505.4",
"protein_id": null,
"transcript_support_level": 4,
"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": 570,
"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": 3,
"intron_rank_end": null,
"gene_symbol": "ENSG00000257545",
"gene_hgnc_id": null,
"hgvs_c": "n.367-28452A>G",
"hgvs_p": null,
"transcript": "ENST00000652234.1",
"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": 1758,
"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": "ENSG00000257545",
"gene_hgnc_id": null,
"hgvs_c": "n.252-14254A>G",
"hgvs_p": null,
"transcript": "ENST00000716380.1",
"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": 832,
"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": 5,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "ENSG00000257545",
"gene_hgnc_id": null,
"hgvs_c": "n.294-14254A>G",
"hgvs_p": null,
"transcript": "ENST00000716382.1",
"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": 869,
"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": "LOC100287944",
"gene_hgnc_id": null,
"hgvs_c": "n.142+78267A>G",
"hgvs_p": null,
"transcript": "NR_040246.1",
"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": 569,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "RFX4",
"gene_hgnc_id": 9985,
"dbsnp": "rs10778502",
"frequency_reference_population": 0.37470257,
"hom_count_reference_population": 115197,
"allele_count_reference_population": 604686,
"gnomad_exomes_af": 0.371817,
"gnomad_genomes_af": 0.402463,
"gnomad_exomes_ac": 543531,
"gnomad_genomes_ac": 61155,
"gnomad_exomes_homalt": 102486,
"gnomad_genomes_homalt": 12711,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.8299999833106995,
"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": -0.83,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -4.058,
"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": -13,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP7,BA1",
"acmg_by_gene": [
{
"score": -13,
"benign_score": 13,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP7",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000392842.6",
"gene_symbol": "RFX4",
"hgnc_id": 9985,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.810T>C",
"hgvs_p": "p.Thr270Thr"
},
{
"score": -12,
"benign_score": 12,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000549203.2",
"gene_symbol": "ENSG00000257545",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.142+78267A>G",
"hgvs_p": null
},
{
"score": -12,
"benign_score": 12,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "NR_040246.1",
"gene_symbol": "LOC100287944",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.142+78267A>G",
"hgvs_p": null
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}