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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: 2-240742952-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=240742952&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 1,
"criteria": [
"BP4"
],
"effects": [
"missense_variant"
],
"gene_symbol": "KIF1A",
"hgnc_id": 888,
"hgvs_c": "c.3692G>T",
"hgvs_p": "p.Arg1231Leu",
"inheritance_mode": "AR,AD",
"pathogenic_score": 0,
"score": -1,
"transcript": "NM_001379631.1",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4",
"acmg_score": -1,
"allele_count_reference_population": 33,
"alphamissense_prediction": null,
"alphamissense_score": 0.6152,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.2,
"chr": "2",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": " autosomal dominant 9, hereditary sensory, type 2C,Hereditary spastic paraplegia 30,Intellectual disability,Neuropathy",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.3323369324207306,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 1791,
"aa_ref": "R",
"aa_start": 1206,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9131,
"cdna_start": 3775,
"cds_end": null,
"cds_length": 5376,
"cds_start": 3617,
"consequences": [
"missense_variant"
],
"exon_count": 49,
"exon_rank": 34,
"exon_rank_end": null,
"feature": "NM_001244008.2",
"gene_hgnc_id": 888,
"gene_symbol": "KIF1A",
"hgvs_c": "c.3617G>T",
"hgvs_p": "p.Arg1206Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000498729.9",
"protein_coding": true,
"protein_id": "NP_001230937.1",
"strand": false,
"transcript": "NM_001244008.2",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 1791,
"aa_ref": "R",
"aa_start": 1206,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 9131,
"cdna_start": 3775,
"cds_end": null,
"cds_length": 5376,
"cds_start": 3617,
"consequences": [
"missense_variant"
],
"exon_count": 49,
"exon_rank": 34,
"exon_rank_end": null,
"feature": "ENST00000498729.9",
"gene_hgnc_id": 888,
"gene_symbol": "KIF1A",
"hgvs_c": "c.3617G>T",
"hgvs_p": "p.Arg1206Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001244008.2",
"protein_coding": true,
"protein_id": "ENSP00000438388.1",
"strand": false,
"transcript": "ENST00000498729.9",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 7507,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 16,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000492812.6",
"gene_hgnc_id": 888,
"gene_symbol": "KIF1A",
"hgvs_c": "n.779G>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000492812.6",
"transcript_support_level": 1
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 1894,
"aa_ref": "R",
"aa_start": 1206,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9151,
"cdna_start": 3775,
"cds_end": null,
"cds_length": 5685,
"cds_start": 3617,
"consequences": [
"missense_variant"
],
"exon_count": 49,
"exon_rank": 34,
"exon_rank_end": null,
"feature": "ENST00000675932.2",
"gene_hgnc_id": 888,
"gene_symbol": "KIF1A",
"hgvs_c": "c.3617G>T",
"hgvs_p": "p.Arg1206Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000502786.2",
"strand": false,
"transcript": "ENST00000675932.2",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 1834,
"aa_ref": "R",
"aa_start": 1249,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9260,
"cdna_start": 3904,
"cds_end": null,
"cds_length": 5505,
"cds_start": 3746,
"consequences": [
"missense_variant"
],
"exon_count": 50,
"exon_rank": 35,
"exon_rank_end": null,
"feature": "ENST00000675314.2",
"gene_hgnc_id": 888,
"gene_symbol": "KIF1A",
"hgvs_c": "c.3746G>T",
"hgvs_p": "p.Arg1249Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000502584.2",
"strand": false,
"transcript": "ENST00000675314.2",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 1833,
"aa_ref": "R",
"aa_start": 1248,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9257,
"cdna_start": 3901,
"cds_end": null,
"cds_length": 5502,
"cds_start": 3743,
"consequences": [
"missense_variant"
],
"exon_count": 50,
"exon_rank": 35,
"exon_rank_end": null,
"feature": "ENST00000674607.2",
"gene_hgnc_id": 888,
"gene_symbol": "KIF1A",
"hgvs_c": "c.3743G>T",
"hgvs_p": "p.Arg1248Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000501825.2",
"strand": false,
"transcript": "ENST00000674607.2",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 1825,
"aa_ref": "R",
"aa_start": 1231,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9545,
"cdna_start": 4162,
"cds_end": null,
"cds_length": 5478,
"cds_start": 3692,
"consequences": [
"missense_variant"
],
"exon_count": 51,
"exon_rank": 35,
"exon_rank_end": null,
"feature": "ENST00000448728.2",
"gene_hgnc_id": 888,
"gene_symbol": "KIF1A",
"hgvs_c": "c.3692G>T",
"hgvs_p": "p.Arg1231Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000398686.2",
"strand": false,
"transcript": "ENST00000448728.2",
"transcript_support_level": 5
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 1816,
"aa_ref": "R",
"aa_start": 1231,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9206,
"cdna_start": 3850,
"cds_end": null,
"cds_length": 5451,
"cds_start": 3692,
"consequences": [
"missense_variant"
],
"exon_count": 49,
"exon_rank": 34,
"exon_rank_end": null,
"feature": "NM_001379631.1",
"gene_hgnc_id": 888,
"gene_symbol": "KIF1A",
"hgvs_c": "c.3692G>T",
"hgvs_p": "p.Arg1231Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001366560.1",
"strand": false,
"transcript": "NM_001379631.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 1808,
"aa_ref": "R",
"aa_start": 1223,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9177,
"cdna_start": 3822,
"cds_end": null,
"cds_length": 5427,
"cds_start": 3668,
"consequences": [
"missense_variant"
],
"exon_count": 49,
"exon_rank": 34,
"exon_rank_end": null,
"feature": "ENST00000675126.2",
"gene_hgnc_id": 888,
"gene_symbol": "KIF1A",
"hgvs_c": "c.3668G>T",
"hgvs_p": "p.Arg1223Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000501874.2",
"strand": false,
"transcript": "ENST00000675126.2",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 1803,
"aa_ref": "R",
"aa_start": 1218,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9167,
"cdna_start": 3811,
"cds_end": null,
"cds_length": 5412,
"cds_start": 3653,
"consequences": [
"missense_variant"
],
"exon_count": 49,
"exon_rank": 34,
"exon_rank_end": null,
"feature": "ENST00000674975.2",
"gene_hgnc_id": 888,
"gene_symbol": "KIF1A",
"hgvs_c": "c.3653G>T",
"hgvs_p": "p.Arg1218Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000502241.2",
"strand": false,
"transcript": "ENST00000674975.2",
"transcript_support_level": null
},
{
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"aa_length": 1799,
"aa_ref": "R",
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"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5647,
"cdna_start": 3864,
"cds_end": null,
"cds_length": 5400,
"cds_start": 3617,
"consequences": [
"missense_variant"
],
"exon_count": 50,
"exon_rank": 34,
"exon_rank_end": null,
"feature": "ENST00000404283.9",
"gene_hgnc_id": 888,
"gene_symbol": "KIF1A",
"hgvs_c": "c.3617G>T",
"hgvs_p": "p.Arg1206Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000384231.5",
"strand": false,
"transcript": "ENST00000404283.9",
"transcript_support_level": 5
},
{
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"aa_length": 1796,
"aa_ref": "R",
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"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9146,
"cdna_start": 3775,
"cds_end": null,
"cds_length": 5391,
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"consequences": [
"missense_variant"
],
"exon_count": 49,
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"exon_rank_end": null,
"feature": "ENST00000676050.2",
"gene_hgnc_id": 888,
"gene_symbol": "KIF1A",
"hgvs_c": "c.3617G>T",
"hgvs_p": "p.Arg1206Leu",
"intron_rank": null,
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"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000501938.2",
"strand": false,
"transcript": "ENST00000676050.2",
"transcript_support_level": null
},
{
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"aa_ref": "R",
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"cdna_start": 3748,
"cds_end": null,
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"cds_start": 3590,
"consequences": [
"missense_variant"
],
"exon_count": 49,
"exon_rank": 33,
"exon_rank_end": null,
"feature": "NM_001379642.1",
"gene_hgnc_id": 888,
"gene_symbol": "KIF1A",
"hgvs_c": "c.3590G>T",
"hgvs_p": "p.Arg1197Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001366571.1",
"strand": false,
"transcript": "NM_001379642.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
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"aa_length": 1791,
"aa_ref": "R",
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"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9257,
"cdna_start": 3901,
"cds_end": null,
"cds_length": 5376,
"cds_start": 3617,
"consequences": [
"missense_variant"
],
"exon_count": 49,
"exon_rank": 34,
"exon_rank_end": null,
"feature": "ENST00000647572.2",
"gene_hgnc_id": 888,
"gene_symbol": "KIF1A",
"hgvs_c": "c.3617G>T",
"hgvs_p": "p.Arg1206Leu",
"intron_rank": null,
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"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000497953.2",
"strand": false,
"transcript": "ENST00000647572.2",
"transcript_support_level": null
},
{
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"aa_ref": "R",
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"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9064,
"cdna_start": 3708,
"cds_end": null,
"cds_length": 5376,
"cds_start": 3617,
"consequences": [
"missense_variant"
],
"exon_count": 49,
"exon_rank": 34,
"exon_rank_end": null,
"feature": "ENST00000674664.2",
"gene_hgnc_id": 888,
"gene_symbol": "KIF1A",
"hgvs_c": "c.3617G>T",
"hgvs_p": "p.Arg1206Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000501778.2",
"strand": false,
"transcript": "ENST00000674664.2",
"transcript_support_level": null
},
{
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"aa_ref": "R",
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"biotype": "protein_coding",
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"cdna_end": null,
"cdna_length": 9359,
"cdna_start": 4003,
"cds_end": null,
"cds_length": 5376,
"cds_start": 3617,
"consequences": [
"missense_variant"
],
"exon_count": 49,
"exon_rank": 34,
"exon_rank_end": null,
"feature": "ENST00000674907.2",
"gene_hgnc_id": 888,
"gene_symbol": "KIF1A",
"hgvs_c": "c.3617G>T",
"hgvs_p": "p.Arg1206Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000502048.2",
"strand": false,
"transcript": "ENST00000674907.2",
"transcript_support_level": null
},
{
"aa_alt": "L",
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"aa_ref": "R",
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"biotype": "protein_coding",
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"cdna_end": null,
"cdna_length": 9204,
"cdna_start": 3848,
"cds_end": null,
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"consequences": [
"missense_variant"
],
"exon_count": 49,
"exon_rank": 34,
"exon_rank_end": null,
"feature": "ENST00000675152.2",
"gene_hgnc_id": 888,
"gene_symbol": "KIF1A",
"hgvs_c": "c.3617G>T",
"hgvs_p": "p.Arg1206Leu",
"intron_rank": null,
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"mane_plus": null,
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"protein_coding": true,
"protein_id": "ENSP00000501849.2",
"strand": false,
"transcript": "ENST00000675152.2",
"transcript_support_level": null
},
{
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"biotype": "protein_coding",
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"cdna_start": 3751,
"cds_end": null,
"cds_length": 5376,
"cds_start": 3617,
"consequences": [
"missense_variant"
],
"exon_count": 49,
"exon_rank": 34,
"exon_rank_end": null,
"feature": "ENST00000675940.2",
"gene_hgnc_id": 888,
"gene_symbol": "KIF1A",
"hgvs_c": "c.3617G>T",
"hgvs_p": "p.Arg1206Leu",
"intron_rank": null,
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"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000501962.2",
"strand": false,
"transcript": "ENST00000675940.2",
"transcript_support_level": null
},
{
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"aa_ref": "R",
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"biotype": "protein_coding",
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"cdna_start": 3724,
"cds_end": null,
"cds_length": 5352,
"cds_start": 3566,
"consequences": [
"missense_variant"
],
"exon_count": 49,
"exon_rank": 33,
"exon_rank_end": null,
"feature": "NM_001379632.1",
"gene_hgnc_id": 888,
"gene_symbol": "KIF1A",
"hgvs_c": "c.3566G>T",
"hgvs_p": "p.Arg1189Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001366561.1",
"strand": false,
"transcript": "NM_001379632.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
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"aa_length": 1782,
"aa_ref": "R",
"aa_start": 1197,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9104,
"cdna_start": 3748,
"cds_end": null,
"cds_length": 5349,
"cds_start": 3590,
"consequences": [
"missense_variant"
],
"exon_count": 48,
"exon_rank": 33,
"exon_rank_end": null,
"feature": "NM_001379633.1",
"gene_hgnc_id": 888,
"gene_symbol": "KIF1A",
"hgvs_c": "c.3590G>T",
"hgvs_p": "p.Arg1197Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001366562.1",
"strand": false,
"transcript": "NM_001379633.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 1782,
"aa_ref": "R",
"aa_start": 1197,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9130,
"cdna_start": 3774,
"cds_end": null,
"cds_length": 5349,
"cds_start": 3590,
"consequences": [
"missense_variant"
],
"exon_count": 48,
"exon_rank": 33,
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"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs369849214",
"effect": "missense_variant",
"frequency_reference_population": 0.000020477511,
"gene_hgnc_id": 888,
"gene_symbol": "KIF1A",
"gnomad_exomes_ac": 32,
"gnomad_exomes_af": 0.0000219272,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 1,
"gnomad_genomes_af": 0.00000657237,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "Hereditary spastic paraplegia 30;Neuropathy, hereditary sensory, type 2C;Intellectual disability, autosomal dominant 9",
"phylop100way_prediction": "Benign",
"phylop100way_score": 1.832,
"pos": 240742952,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.284,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.019999999552965164,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.02,
"transcript": "NM_001379631.1"
}
]
}