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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: 1-151343848-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=151343848&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 151343848,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_000449.4",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFX5",
"gene_hgnc_id": 9986,
"hgvs_c": "c.590G>A",
"hgvs_p": "p.Arg197Gln",
"transcript": "NM_001025603.2",
"protein_id": "NP_001020774.1",
"transcript_support_level": null,
"aa_start": 197,
"aa_end": null,
"aa_length": 616,
"cds_start": 590,
"cds_end": null,
"cds_length": 1851,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000452671.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001025603.2"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFX5",
"gene_hgnc_id": 9986,
"hgvs_c": "c.590G>A",
"hgvs_p": "p.Arg197Gln",
"transcript": "ENST00000452671.7",
"protein_id": "ENSP00000389130.2",
"transcript_support_level": 1,
"aa_start": 197,
"aa_end": null,
"aa_length": 616,
"cds_start": 590,
"cds_end": null,
"cds_length": 1851,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001025603.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000452671.7"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFX5",
"gene_hgnc_id": 9986,
"hgvs_c": "c.590G>A",
"hgvs_p": "p.Arg197Gln",
"transcript": "ENST00000290524.8",
"protein_id": "ENSP00000290524.4",
"transcript_support_level": 1,
"aa_start": 197,
"aa_end": null,
"aa_length": 616,
"cds_start": 590,
"cds_end": null,
"cds_length": 1851,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000290524.8"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFX5",
"gene_hgnc_id": 9986,
"hgvs_c": "c.590G>A",
"hgvs_p": "p.Arg197Gln",
"transcript": "NM_000449.4",
"protein_id": "NP_000440.1",
"transcript_support_level": null,
"aa_start": 197,
"aa_end": null,
"aa_length": 616,
"cds_start": 590,
"cds_end": null,
"cds_length": 1851,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_000449.4"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFX5",
"gene_hgnc_id": 9986,
"hgvs_c": "c.590G>A",
"hgvs_p": "p.Arg197Gln",
"transcript": "NM_001379412.1",
"protein_id": "NP_001366341.1",
"transcript_support_level": null,
"aa_start": 197,
"aa_end": null,
"aa_length": 616,
"cds_start": 590,
"cds_end": null,
"cds_length": 1851,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001379412.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFX5",
"gene_hgnc_id": 9986,
"hgvs_c": "c.590G>A",
"hgvs_p": "p.Arg197Gln",
"transcript": "NM_001379413.1",
"protein_id": "NP_001366342.1",
"transcript_support_level": null,
"aa_start": 197,
"aa_end": null,
"aa_length": 616,
"cds_start": 590,
"cds_end": null,
"cds_length": 1851,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001379413.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFX5",
"gene_hgnc_id": 9986,
"hgvs_c": "c.590G>A",
"hgvs_p": "p.Arg197Gln",
"transcript": "NM_001379414.1",
"protein_id": "NP_001366343.1",
"transcript_support_level": null,
"aa_start": 197,
"aa_end": null,
"aa_length": 616,
"cds_start": 590,
"cds_end": null,
"cds_length": 1851,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001379414.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFX5",
"gene_hgnc_id": 9986,
"hgvs_c": "c.590G>A",
"hgvs_p": "p.Arg197Gln",
"transcript": "NM_001379415.1",
"protein_id": "NP_001366344.1",
"transcript_support_level": null,
"aa_start": 197,
"aa_end": null,
"aa_length": 616,
"cds_start": 590,
"cds_end": null,
"cds_length": 1851,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001379415.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFX5",
"gene_hgnc_id": 9986,
"hgvs_c": "c.590G>A",
"hgvs_p": "p.Arg197Gln",
"transcript": "NM_001379416.1",
"protein_id": "NP_001366345.1",
"transcript_support_level": null,
"aa_start": 197,
"aa_end": null,
"aa_length": 616,
"cds_start": 590,
"cds_end": null,
"cds_length": 1851,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001379416.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFX5",
"gene_hgnc_id": 9986,
"hgvs_c": "c.590G>A",
"hgvs_p": "p.Arg197Gln",
"transcript": "NM_001379417.1",
"protein_id": "NP_001366346.1",
"transcript_support_level": null,
"aa_start": 197,
"aa_end": null,
"aa_length": 616,
"cds_start": 590,
"cds_end": null,
"cds_length": 1851,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001379417.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFX5",
"gene_hgnc_id": 9986,
"hgvs_c": "c.590G>A",
"hgvs_p": "p.Arg197Gln",
"transcript": "NM_001379418.1",
"protein_id": "NP_001366347.1",
"transcript_support_level": null,
"aa_start": 197,
"aa_end": null,
"aa_length": 616,
"cds_start": 590,
"cds_end": null,
"cds_length": 1851,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001379418.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFX5",
"gene_hgnc_id": 9986,
"hgvs_c": "c.590G>A",
"hgvs_p": "p.Arg197Gln",
"transcript": "ENST00000368870.6",
"protein_id": "ENSP00000357864.2",
"transcript_support_level": 5,
"aa_start": 197,
"aa_end": null,
"aa_length": 616,
"cds_start": 590,
"cds_end": null,
"cds_length": 1851,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000368870.6"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFX5",
"gene_hgnc_id": 9986,
"hgvs_c": "c.590G>A",
"hgvs_p": "p.Arg197Gln",
"transcript": "ENST00000882448.1",
"protein_id": "ENSP00000552507.1",
"transcript_support_level": null,
"aa_start": 197,
"aa_end": null,
"aa_length": 616,
"cds_start": 590,
"cds_end": null,
"cds_length": 1851,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000882448.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFX5",
"gene_hgnc_id": 9986,
"hgvs_c": "c.590G>A",
"hgvs_p": "p.Arg197Gln",
"transcript": "ENST00000882449.1",
"protein_id": "ENSP00000552508.1",
"transcript_support_level": null,
"aa_start": 197,
"aa_end": null,
"aa_length": 616,
"cds_start": 590,
"cds_end": null,
"cds_length": 1851,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000882449.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFX5",
"gene_hgnc_id": 9986,
"hgvs_c": "c.590G>A",
"hgvs_p": "p.Arg197Gln",
"transcript": "ENST00000882450.1",
"protein_id": "ENSP00000552509.1",
"transcript_support_level": null,
"aa_start": 197,
"aa_end": null,
"aa_length": 616,
"cds_start": 590,
"cds_end": null,
"cds_length": 1851,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000882450.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFX5",
"gene_hgnc_id": 9986,
"hgvs_c": "c.590G>A",
"hgvs_p": "p.Arg197Gln",
"transcript": "ENST00000939317.1",
"protein_id": "ENSP00000609376.1",
"transcript_support_level": null,
"aa_start": 197,
"aa_end": null,
"aa_length": 616,
"cds_start": 590,
"cds_end": null,
"cds_length": 1851,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000939317.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFX5",
"gene_hgnc_id": 9986,
"hgvs_c": "c.590G>A",
"hgvs_p": "p.Arg197Gln",
"transcript": "ENST00000939319.1",
"protein_id": "ENSP00000609378.1",
"transcript_support_level": null,
"aa_start": 197,
"aa_end": null,
"aa_length": 616,
"cds_start": 590,
"cds_end": null,
"cds_length": 1851,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000939319.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFX5",
"gene_hgnc_id": 9986,
"hgvs_c": "c.590G>A",
"hgvs_p": "p.Arg197Gln",
"transcript": "ENST00000943235.1",
"protein_id": "ENSP00000613294.1",
"transcript_support_level": null,
"aa_start": 197,
"aa_end": null,
"aa_length": 616,
"cds_start": 590,
"cds_end": null,
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"cdna_start": null,
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"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000943235.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFX5",
"gene_hgnc_id": 9986,
"hgvs_c": "c.590G>A",
"hgvs_p": "p.Arg197Gln",
"transcript": "ENST00000939315.1",
"protein_id": "ENSP00000609374.1",
"transcript_support_level": null,
"aa_start": 197,
"aa_end": null,
"aa_length": 615,
"cds_start": 590,
"cds_end": null,
"cds_length": 1848,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000939315.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFX5",
"gene_hgnc_id": 9986,
"hgvs_c": "c.578G>A",
"hgvs_p": "p.Arg193Gln",
"transcript": "ENST00000882446.1",
"protein_id": "ENSP00000552505.1",
"transcript_support_level": null,
"aa_start": 193,
"aa_end": null,
"aa_length": 612,
"cds_start": 578,
"cds_end": null,
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"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000882446.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFX5",
"gene_hgnc_id": 9986,
"hgvs_c": "c.590G>A",
"hgvs_p": "p.Arg197Gln",
"transcript": "ENST00000392746.7",
"protein_id": "ENSP00000376502.3",
"transcript_support_level": 5,
"aa_start": 197,
"aa_end": null,
"aa_length": 595,
"cds_start": 590,
"cds_end": null,
"cds_length": 1790,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000392746.7"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFX5",
"gene_hgnc_id": 9986,
"hgvs_c": "c.470G>A",
"hgvs_p": "p.Arg157Gln",
"transcript": "NM_001379419.1",
"protein_id": "NP_001366348.1",
"transcript_support_level": null,
"aa_start": 157,
"aa_end": null,
"aa_length": 576,
"cds_start": 470,
"cds_end": null,
"cds_length": 1731,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001379419.1"
},
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],
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"computational_score_selected": 0.004905492067337036,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.091,
"revel_prediction": "Benign",
"alphamissense_score": 0.0833,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.38,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 3.625,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.02,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": null,
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"apogee2_prediction": null,
"mitotip_score": null,
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"acmg_score": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BS1,BS2",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_000449.4",
"gene_symbol": "RFX5",
"hgnc_id": 9986,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.590G>A",
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{
"score": -16,
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"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000811547.1",
"gene_symbol": "RFX5-AS1",
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"effects": [
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],
"inheritance_mode": "",
"hgvs_c": "n.530-3784C>T",
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}
],
"clinvar_disease": "MHC class II deficiency,RFX5-related disorder,not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:5",
"phenotype_combined": "MHC class II deficiency|not specified|not provided|RFX5-related disorder",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}