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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: 9-3225104-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=3225104&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 13,
"criteria": [
"BP4_Strong",
"BP6",
"BS1",
"BS2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "RFX3",
"hgnc_id": 9984,
"hgvs_c": "c.2251G>A",
"hgvs_p": "p.Val751Ile",
"inheritance_mode": "AD",
"pathogenic_score": 0,
"score": -13,
"transcript": "NM_001377999.1",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6,BS1,BS2",
"acmg_score": -13,
"allele_count_reference_population": 2747,
"alphamissense_prediction": null,
"alphamissense_score": 0.0657,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.42,
"chr": "9",
"clinvar_classification": "Likely benign",
"clinvar_disease": "RFX3-related disorder",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.005207628011703491,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 749,
"aa_ref": "V",
"aa_start": 730,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9258,
"cdna_start": 2451,
"cds_end": null,
"cds_length": 2250,
"cds_start": 2188,
"consequences": [
"missense_variant"
],
"exon_count": 17,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "NM_001282116.2",
"gene_hgnc_id": 9984,
"gene_symbol": "RFX3",
"hgvs_c": "c.2188G>A",
"hgvs_p": "p.Val730Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000617270.5",
"protein_coding": true,
"protein_id": "NP_001269045.1",
"strand": false,
"transcript": "NM_001282116.2",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 749,
"aa_ref": "V",
"aa_start": 730,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 9258,
"cdna_start": 2451,
"cds_end": null,
"cds_length": 2250,
"cds_start": 2188,
"consequences": [
"missense_variant"
],
"exon_count": 17,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "ENST00000617270.5",
"gene_hgnc_id": 9984,
"gene_symbol": "RFX3",
"hgvs_c": "c.2188G>A",
"hgvs_p": "p.Val730Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001282116.2",
"protein_coding": true,
"protein_id": "ENSP00000482598.1",
"strand": false,
"transcript": "ENST00000617270.5",
"transcript_support_level": 2
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 749,
"aa_ref": "V",
"aa_start": 730,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9307,
"cdna_start": 2500,
"cds_end": null,
"cds_length": 2250,
"cds_start": 2188,
"consequences": [
"missense_variant"
],
"exon_count": 18,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "ENST00000382004.7",
"gene_hgnc_id": 9984,
"gene_symbol": "RFX3",
"hgvs_c": "c.2188G>A",
"hgvs_p": "p.Val730Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000371434.3",
"strand": false,
"transcript": "ENST00000382004.7",
"transcript_support_level": 1
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 770,
"aa_ref": "V",
"aa_start": 751,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9321,
"cdna_start": 2514,
"cds_end": null,
"cds_length": 2313,
"cds_start": 2251,
"consequences": [
"missense_variant"
],
"exon_count": 18,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "NM_001377999.1",
"gene_hgnc_id": 9984,
"gene_symbol": "RFX3",
"hgvs_c": "c.2251G>A",
"hgvs_p": "p.Val751Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001364928.1",
"strand": false,
"transcript": "NM_001377999.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 770,
"aa_ref": "V",
"aa_start": 751,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4933,
"cdna_start": 2476,
"cds_end": null,
"cds_length": 2313,
"cds_start": 2251,
"consequences": [
"missense_variant"
],
"exon_count": 18,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "ENST00000968852.1",
"gene_hgnc_id": 9984,
"gene_symbol": "RFX3",
"hgvs_c": "c.2251G>A",
"hgvs_p": "p.Val751Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000638911.1",
"strand": false,
"transcript": "ENST00000968852.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 770,
"aa_ref": "V",
"aa_start": 751,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4879,
"cdna_start": 2431,
"cds_end": null,
"cds_length": 2313,
"cds_start": 2251,
"consequences": [
"missense_variant"
],
"exon_count": 18,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "ENST00000968853.1",
"gene_hgnc_id": 9984,
"gene_symbol": "RFX3",
"hgvs_c": "c.2251G>A",
"hgvs_p": "p.Val751Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000638912.1",
"strand": false,
"transcript": "ENST00000968853.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 749,
"aa_ref": "V",
"aa_start": 730,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9325,
"cdna_start": 2518,
"cds_end": null,
"cds_length": 2250,
"cds_start": 2188,
"consequences": [
"missense_variant"
],
"exon_count": 18,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "NM_134428.3",
"gene_hgnc_id": 9984,
"gene_symbol": "RFX3",
"hgvs_c": "c.2188G>A",
"hgvs_p": "p.Val730Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_602304.1",
"strand": false,
"transcript": "NM_134428.3",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 749,
"aa_ref": "V",
"aa_start": 730,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5012,
"cdna_start": 2555,
"cds_end": null,
"cds_length": 2250,
"cds_start": 2188,
"consequences": [
"missense_variant"
],
"exon_count": 18,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "ENST00000876564.1",
"gene_hgnc_id": 9984,
"gene_symbol": "RFX3",
"hgvs_c": "c.2188G>A",
"hgvs_p": "p.Val730Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000546623.1",
"strand": false,
"transcript": "ENST00000876564.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 749,
"aa_ref": "V",
"aa_start": 730,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4805,
"cdna_start": 2348,
"cds_end": null,
"cds_length": 2250,
"cds_start": 2188,
"consequences": [
"missense_variant"
],
"exon_count": 17,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "ENST00000876565.1",
"gene_hgnc_id": 9984,
"gene_symbol": "RFX3",
"hgvs_c": "c.2188G>A",
"hgvs_p": "p.Val730Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000546624.1",
"strand": false,
"transcript": "ENST00000876565.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 749,
"aa_ref": "V",
"aa_start": 730,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3884,
"cdna_start": 2423,
"cds_end": null,
"cds_length": 2250,
"cds_start": 2188,
"consequences": [
"missense_variant"
],
"exon_count": 19,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "ENST00000876567.1",
"gene_hgnc_id": 9984,
"gene_symbol": "RFX3",
"hgvs_c": "c.2188G>A",
"hgvs_p": "p.Val730Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000546626.1",
"strand": false,
"transcript": "ENST00000876567.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 749,
"aa_ref": "V",
"aa_start": 730,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5362,
"cdna_start": 2574,
"cds_end": null,
"cds_length": 2250,
"cds_start": 2188,
"consequences": [
"missense_variant"
],
"exon_count": 18,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "ENST00000968851.1",
"gene_hgnc_id": 9984,
"gene_symbol": "RFX3",
"hgvs_c": "c.2188G>A",
"hgvs_p": "p.Val730Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000638910.1",
"strand": false,
"transcript": "ENST00000968851.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
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"aa_length": 724,
"aa_ref": "V",
"aa_start": 705,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4311,
"cdna_start": 2367,
"cds_end": null,
"cds_length": 2175,
"cds_start": 2113,
"consequences": [
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],
"exon_count": 16,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000876566.1",
"gene_hgnc_id": 9984,
"gene_symbol": "RFX3",
"hgvs_c": "c.2113G>A",
"hgvs_p": "p.Val705Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000546625.1",
"strand": false,
"transcript": "ENST00000876566.1",
"transcript_support_level": null
},
{
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"aa_length": 800,
"aa_ref": "V",
"aa_start": 781,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 10430,
"cdna_start": 3623,
"cds_end": null,
"cds_length": 2403,
"cds_start": 2341,
"consequences": [
"missense_variant"
],
"exon_count": 20,
"exon_rank": 20,
"exon_rank_end": null,
"feature": "XM_024447630.2",
"gene_hgnc_id": 9984,
"gene_symbol": "RFX3",
"hgvs_c": "c.2341G>A",
"hgvs_p": "p.Val781Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_024303398.1",
"strand": false,
"transcript": "XM_024447630.2",
"transcript_support_level": null
},
{
"aa_alt": "I",
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"aa_length": 800,
"aa_ref": "V",
"aa_start": 781,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 10298,
"cdna_start": 3491,
"cds_end": null,
"cds_length": 2403,
"cds_start": 2341,
"consequences": [
"missense_variant"
],
"exon_count": 19,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "XM_024447631.2",
"gene_hgnc_id": 9984,
"gene_symbol": "RFX3",
"hgvs_c": "c.2341G>A",
"hgvs_p": "p.Val781Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_024303399.1",
"strand": false,
"transcript": "XM_024447631.2",
"transcript_support_level": null
},
{
"aa_alt": "I",
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"aa_length": 800,
"aa_ref": "V",
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"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 12415,
"cdna_start": 5608,
"cds_end": null,
"cds_length": 2403,
"cds_start": 2341,
"consequences": [
"missense_variant"
],
"exon_count": 19,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "XM_047423687.1",
"gene_hgnc_id": 9984,
"gene_symbol": "RFX3",
"hgvs_c": "c.2341G>A",
"hgvs_p": "p.Val781Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047279643.1",
"strand": false,
"transcript": "XM_047423687.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 800,
"aa_ref": "V",
"aa_start": 781,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 10808,
"cdna_start": 4001,
"cds_end": null,
"cds_length": 2403,
"cds_start": 2341,
"consequences": [
"missense_variant"
],
"exon_count": 20,
"exon_rank": 20,
"exon_rank_end": null,
"feature": "XM_047423688.1",
"gene_hgnc_id": 9984,
"gene_symbol": "RFX3",
"hgvs_c": "c.2341G>A",
"hgvs_p": "p.Val781Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047279644.1",
"strand": false,
"transcript": "XM_047423688.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 780,
"aa_ref": "V",
"aa_start": 761,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 10588,
"cdna_start": 3781,
"cds_end": null,
"cds_length": 2343,
"cds_start": 2281,
"consequences": [
"missense_variant"
],
"exon_count": 18,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "XM_006716840.3",
"gene_hgnc_id": 9984,
"gene_symbol": "RFX3",
"hgvs_c": "c.2281G>A",
"hgvs_p": "p.Val761Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_006716903.1",
"strand": false,
"transcript": "XM_006716840.3",
"transcript_support_level": null
},
{
"aa_alt": "I",
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"aa_ref": "V",
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"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 12352,
"cdna_start": 5545,
"cds_end": null,
"cds_length": 2340,
"cds_start": 2278,
"consequences": [
"missense_variant"
],
"exon_count": 18,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "XM_047423689.1",
"gene_hgnc_id": 9984,
"gene_symbol": "RFX3",
"hgvs_c": "c.2278G>A",
"hgvs_p": "p.Val760Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047279645.1",
"strand": false,
"transcript": "XM_047423689.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
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"aa_length": 776,
"aa_ref": "V",
"aa_start": 757,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9404,
"cdna_start": 2597,
"cds_end": null,
"cds_length": 2331,
"cds_start": 2269,
"consequences": [
"missense_variant"
],
"exon_count": 19,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "XM_024447632.2",
"gene_hgnc_id": 9984,
"gene_symbol": "RFX3",
"hgvs_c": "c.2269G>A",
"hgvs_p": "p.Val757Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_024303400.1",
"strand": false,
"transcript": "XM_024447632.2",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 776,
"aa_ref": "V",
"aa_start": 757,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 12025,
"cdna_start": 5218,
"cds_end": null,
"cds_length": 2331,
"cds_start": 2269,
"consequences": [
"missense_variant"
],
"exon_count": 18,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "XM_047423690.1",
"gene_hgnc_id": 9984,
"gene_symbol": "RFX3",
"hgvs_c": "c.2269G>A",
"hgvs_p": "p.Val757Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047279646.1",
"strand": false,
"transcript": "XM_047423690.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 775,
"aa_ref": "V",
"aa_start": 756,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 12340,
"cdna_start": 5533,
"cds_end": null,
"cds_length": 2328,
"cds_start": 2266,
"consequences": [
"missense_variant"
],
"exon_count": 18,
"exon_rank": 18,
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