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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: 12-106689354-A-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=106689354&ref=A&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 106689354,
"ref": "A",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_001206691.2",
"consequences": [
{
"aa_ref": "N",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFX4",
"gene_hgnc_id": 9985,
"hgvs_c": "c.659A>C",
"hgvs_p": "p.Asn220Thr",
"transcript": "NM_213594.3",
"protein_id": "NP_998759.1",
"transcript_support_level": null,
"aa_start": 220,
"aa_end": null,
"aa_length": 735,
"cds_start": 659,
"cds_end": null,
"cds_length": 2208,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000392842.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_213594.3"
},
{
"aa_ref": "N",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFX4",
"gene_hgnc_id": 9985,
"hgvs_c": "c.659A>C",
"hgvs_p": "p.Asn220Thr",
"transcript": "ENST00000392842.6",
"protein_id": "ENSP00000376585.1",
"transcript_support_level": 1,
"aa_start": 220,
"aa_end": null,
"aa_length": 735,
"cds_start": 659,
"cds_end": null,
"cds_length": 2208,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_213594.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000392842.6"
},
{
"aa_ref": "N",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFX4",
"gene_hgnc_id": 9985,
"hgvs_c": "c.686A>C",
"hgvs_p": "p.Asn229Thr",
"transcript": "ENST00000357881.8",
"protein_id": "ENSP00000350552.4",
"transcript_support_level": 1,
"aa_start": 229,
"aa_end": null,
"aa_length": 744,
"cds_start": 686,
"cds_end": null,
"cds_length": 2235,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000357881.8"
},
{
"aa_ref": "N",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFX4",
"gene_hgnc_id": 9985,
"hgvs_c": "c.377A>C",
"hgvs_p": "p.Asn126Thr",
"transcript": "ENST00000229387.6",
"protein_id": "ENSP00000229387.5",
"transcript_support_level": 1,
"aa_start": 126,
"aa_end": null,
"aa_length": 641,
"cds_start": 377,
"cds_end": null,
"cds_length": 1926,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000229387.6"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFX4",
"gene_hgnc_id": 9985,
"hgvs_c": "n.791A>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": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000536688.5"
},
{
"aa_ref": "N",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFX4",
"gene_hgnc_id": 9985,
"hgvs_c": "c.686A>C",
"hgvs_p": "p.Asn229Thr",
"transcript": "NM_001206691.2",
"protein_id": "NP_001193620.1",
"transcript_support_level": null,
"aa_start": 229,
"aa_end": null,
"aa_length": 744,
"cds_start": 686,
"cds_end": null,
"cds_length": 2235,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001206691.2"
},
{
"aa_ref": "N",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFX4",
"gene_hgnc_id": 9985,
"hgvs_c": "c.659A>C",
"hgvs_p": "p.Asn220Thr",
"transcript": "ENST00000959768.1",
"protein_id": "ENSP00000629827.1",
"transcript_support_level": null,
"aa_start": 220,
"aa_end": null,
"aa_length": 734,
"cds_start": 659,
"cds_end": null,
"cds_length": 2205,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000959768.1"
},
{
"aa_ref": "N",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFX4",
"gene_hgnc_id": 9985,
"hgvs_c": "c.572A>C",
"hgvs_p": "p.Asn191Thr",
"transcript": "ENST00000959769.1",
"protein_id": "ENSP00000629828.1",
"transcript_support_level": null,
"aa_start": 191,
"aa_end": null,
"aa_length": 705,
"cds_start": 572,
"cds_end": null,
"cds_length": 2118,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000959769.1"
},
{
"aa_ref": "N",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFX4",
"gene_hgnc_id": 9985,
"hgvs_c": "c.377A>C",
"hgvs_p": "p.Asn126Thr",
"transcript": "NM_032491.6",
"protein_id": "NP_115880.2",
"transcript_support_level": null,
"aa_start": 126,
"aa_end": null,
"aa_length": 641,
"cds_start": 377,
"cds_end": null,
"cds_length": 1926,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_032491.6"
},
{
"aa_ref": "N",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFX4",
"gene_hgnc_id": 9985,
"hgvs_c": "c.494A>C",
"hgvs_p": "p.Asn165Thr",
"transcript": "ENST00000551640.5",
"protein_id": "ENSP00000448694.1",
"transcript_support_level": 5,
"aa_start": 165,
"aa_end": null,
"aa_length": 255,
"cds_start": 494,
"cds_end": null,
"cds_length": 769,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000551640.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "RFX4",
"gene_hgnc_id": 9985,
"hgvs_c": "c.-33-6929A>C",
"hgvs_p": null,
"transcript": "ENST00000539967.6",
"protein_id": "ENSP00000473326.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 144,
"cds_start": null,
"cds_end": null,
"cds_length": 436,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000539967.6"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFX4",
"gene_hgnc_id": 9985,
"hgvs_c": "n.686A>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": 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": "ENST00000536722.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFX4",
"gene_hgnc_id": 9985,
"hgvs_c": "n.495A>C",
"hgvs_p": null,
"transcript": "ENST00000552866.5",
"protein_id": null,
"transcript_support_level": 4,
"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": "ENST00000552866.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFX4",
"gene_hgnc_id": 9985,
"hgvs_c": "n.*234A>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": 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": "ENST00000552917.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFX4",
"gene_hgnc_id": 9985,
"hgvs_c": "n.*234A>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": 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": "ENST00000552917.1"
},
{
"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+85336T>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": 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": "ENST00000549203.2"
},
{
"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+85336T>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": 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": "ENST00000551505.4"
},
{
"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.367-21383T>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": 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": "ENST00000652234.1"
},
{
"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.252-7185T>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": 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": "ENST00000716380.1"
},
{
"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.294-7185T>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": 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": "ENST00000716382.1"
},
{
"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+85336T>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": 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_040246.1"
}
],
"gene_symbol": "RFX4",
"gene_hgnc_id": 9985,
"dbsnp": "rs368504143",
"frequency_reference_population": 0.00002542024,
"hom_count_reference_population": 0,
"allele_count_reference_population": 41,
"gnomad_exomes_af": 0.0000116394,
"gnomad_genomes_af": 0.000157549,
"gnomad_exomes_ac": 17,
"gnomad_genomes_ac": 24,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.24584749341011047,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.575,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.766,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.05,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 8.911,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.01,
"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_Moderate,BS2",
"acmg_by_gene": [
{
"score": -6,
"benign_score": 6,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "NM_001206691.2",
"gene_symbol": "RFX4",
"hgnc_id": 9985,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.686A>C",
"hgvs_p": "p.Asn229Thr"
},
{
"score": -2,
"benign_score": 2,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate"
],
"verdict": "Likely_benign",
"transcript": "ENST00000549203.2",
"gene_symbol": "ENSG00000257545",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.142+85336T>G",
"hgvs_p": null
},
{
"score": -2,
"benign_score": 2,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate"
],
"verdict": "Likely_benign",
"transcript": "NR_040246.1",
"gene_symbol": "LOC100287944",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.142+85336T>G",
"hgvs_p": null
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}