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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: 2-47806352-ACATATGGTATGTG-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=47806352&ref=ACATATGGTATGTG&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 47806352,
"ref": "ACATATGGTATGTG",
"alt": "A",
"effect": "frameshift_variant,splice_donor_variant,splice_region_variant,intron_variant",
"transcript": "ENST00000234420.11",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH6",
"gene_hgnc_id": 7329,
"hgvs_c": "n.*3145_*3148+9delTATGGTATGTGCA",
"hgvs_p": null,
"transcript": "ENST00000445503.5",
"protein_id": "ENSP00000405294.1",
"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": 4158,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "HM",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant",
"splice_donor_variant",
"splice_region_variant",
"intron_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH6",
"gene_hgnc_id": 7329,
"hgvs_c": "c.3798_3801+9delTATGGTATGTGCA",
"hgvs_p": "p.His1266fs",
"transcript": "NM_000179.3",
"protein_id": "NP_000170.1",
"transcript_support_level": null,
"aa_start": 1266,
"aa_end": null,
"aa_length": 1360,
"cds_start": 3798,
"cds_end": null,
"cds_length": 4083,
"cdna_start": 3887,
"cdna_end": null,
"cdna_length": 4265,
"mane_select": "ENST00000234420.11",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "HM",
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant",
"splice_donor_variant",
"splice_region_variant",
"intron_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH6",
"gene_hgnc_id": 7329,
"hgvs_c": "c.3798_3801+9delTATGGTATGTGCA",
"hgvs_p": "p.His1266fs",
"transcript": "ENST00000234420.11",
"protein_id": "ENSP00000234420.5",
"transcript_support_level": 1,
"aa_start": 1266,
"aa_end": null,
"aa_length": 1360,
"cds_start": 3798,
"cds_end": null,
"cds_length": 4083,
"cdna_start": 3887,
"cdna_end": null,
"cdna_length": 4265,
"mane_select": "NM_000179.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_donor_variant",
"splice_region_variant",
"3_prime_UTR_variant",
"intron_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH6",
"gene_hgnc_id": 7329,
"hgvs_c": "n.*3145_*3148+9delTATGGTATGTGCA",
"hgvs_p": null,
"transcript": "ENST00000445503.5",
"protein_id": "ENSP00000405294.1",
"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": 4158,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FBXO11",
"gene_hgnc_id": 13590,
"hgvs_c": "n.4383_4395delCACATACCATATG",
"hgvs_p": null,
"transcript": "ENST00000682451.1",
"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": 4706,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FBXO11",
"gene_hgnc_id": 13590,
"hgvs_c": "n.4645_4657delCACATACCATATG",
"hgvs_p": null,
"transcript": "ENST00000684712.1",
"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": 4968,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH6",
"gene_hgnc_id": 7329,
"hgvs_c": "n.*563_*566+9delTATGGTATGTGCA",
"hgvs_p": null,
"transcript": "ENST00000700003.1",
"protein_id": "ENSP00000514751.1",
"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": 1593,
"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": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH6",
"gene_hgnc_id": 7329,
"hgvs_c": "n.1967_1979delTATGGTATGTGCA",
"hgvs_p": null,
"transcript": "ENST00000700008.1",
"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": 2401,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "HM",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant",
"splice_donor_variant",
"splice_region_variant",
"intron_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH6",
"gene_hgnc_id": 7329,
"hgvs_c": "c.3894_3897+9delTATGGTATGTGCA",
"hgvs_p": "p.His1298fs",
"transcript": "NM_001406795.1",
"protein_id": "NP_001393724.1",
"transcript_support_level": null,
"aa_start": 1298,
"aa_end": null,
"aa_length": 1392,
"cds_start": 3894,
"cds_end": null,
"cds_length": 4179,
"cdna_start": 3983,
"cdna_end": null,
"cdna_length": 4361,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "HM",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant",
"splice_donor_variant",
"splice_region_variant",
"intron_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH6",
"gene_hgnc_id": 7329,
"hgvs_c": "c.3804_3807+9delTATGGTATGTGCA",
"hgvs_p": "p.His1268fs",
"transcript": "NM_001406813.1",
"protein_id": "NP_001393742.1",
"transcript_support_level": null,
"aa_start": 1268,
"aa_end": null,
"aa_length": 1362,
"cds_start": 3804,
"cds_end": null,
"cds_length": 4089,
"cdna_start": 3893,
"cdna_end": null,
"cdna_length": 4271,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "HM",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant",
"splice_donor_variant",
"splice_region_variant",
"intron_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH6",
"gene_hgnc_id": 7329,
"hgvs_c": "c.3804_3807+9delTATGGTATGTGCA",
"hgvs_p": "p.His1268fs",
"transcript": "ENST00000700002.1",
"protein_id": "ENSP00000514750.1",
"transcript_support_level": null,
"aa_start": 1268,
"aa_end": null,
"aa_length": 1362,
"cds_start": 3804,
"cds_end": null,
"cds_length": 4089,
"cdna_start": 3876,
"cdna_end": null,
"cdna_length": 4233,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "HM",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant",
"splice_donor_variant",
"splice_region_variant",
"intron_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH6",
"gene_hgnc_id": 7329,
"hgvs_c": "c.3798_3801+9delTATGGTATGTGCA",
"hgvs_p": "p.His1266fs",
"transcript": "NM_001406796.1",
"protein_id": "NP_001393725.1",
"transcript_support_level": null,
"aa_start": 1266,
"aa_end": null,
"aa_length": 1360,
"cds_start": 3798,
"cds_end": null,
"cds_length": 4083,
"cdna_start": 3887,
"cdna_end": null,
"cdna_length": 4315,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "HM",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant",
"splice_donor_variant",
"splice_region_variant",
"intron_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH6",
"gene_hgnc_id": 7329,
"hgvs_c": "c.3798_3801+9delTATGGTATGTGCA",
"hgvs_p": "p.His1266fs",
"transcript": "NM_001406809.1",
"protein_id": "NP_001393738.1",
"transcript_support_level": null,
"aa_start": 1266,
"aa_end": null,
"aa_length": 1360,
"cds_start": 3798,
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"cdna_start": 3887,
"cdna_end": null,
"cdna_length": 4318,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "HM",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant",
"splice_donor_variant",
"splice_region_variant",
"intron_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH6",
"gene_hgnc_id": 7329,
"hgvs_c": "c.3798_3801+9delTATGGTATGTGCA",
"hgvs_p": "p.His1266fs",
"transcript": "NM_001406808.1",
"protein_id": "NP_001393737.1",
"transcript_support_level": null,
"aa_start": 1266,
"aa_end": null,
"aa_length": 1337,
"cds_start": 3798,
"cds_end": null,
"cds_length": 4014,
"cdna_start": 3887,
"cdna_end": null,
"cdna_length": 4260,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "HM",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant",
"splice_donor_variant",
"splice_region_variant",
"intron_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH6",
"gene_hgnc_id": 7329,
"hgvs_c": "c.3720_3723+9delTATGGTATGTGCA",
"hgvs_p": "p.His1240fs",
"transcript": "NM_001406804.1",
"protein_id": "NP_001393733.1",
"transcript_support_level": null,
"aa_start": 1240,
"aa_end": null,
"aa_length": 1334,
"cds_start": 3720,
"cds_end": null,
"cds_length": 4005,
"cdna_start": 3864,
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"cdna_length": 4242,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "HM",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant",
"splice_donor_variant",
"splice_region_variant",
"intron_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH6",
"gene_hgnc_id": 7329,
"hgvs_c": "c.3798_3801+9delTATGGTATGTGCA",
"hgvs_p": "p.His1266fs",
"transcript": "NM_001406800.1",
"protein_id": "NP_001393729.1",
"transcript_support_level": null,
"aa_start": 1266,
"aa_end": null,
"aa_length": 1321,
"cds_start": 3798,
"cds_end": null,
"cds_length": 3966,
"cdna_start": 3887,
"cdna_end": null,
"cdna_length": 4252,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "HM",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant",
"splice_donor_variant",
"splice_region_variant",
"intron_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH6",
"gene_hgnc_id": 7329,
"hgvs_c": "c.3894_3897+9delTATGGTATGTGCA",
"hgvs_p": "p.His1298fs",
"transcript": "NM_001406802.1",
"protein_id": "NP_001393731.1",
"transcript_support_level": null,
"aa_start": 1298,
"aa_end": null,
"aa_length": 1304,
"cds_start": 3894,
"cds_end": null,
"cds_length": 3915,
"cdna_start": 3983,
"cdna_end": null,
"cdna_length": 4161,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "HM",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant",
"splice_donor_variant",
"splice_region_variant",
"intron_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH6",
"gene_hgnc_id": 7329,
"hgvs_c": "c.3630_3633+9delTATGGTATGTGCA",
"hgvs_p": "p.His1210fs",
"transcript": "NM_001406826.1",
"protein_id": "NP_001393755.1",
"transcript_support_level": null,
"aa_start": 1210,
"aa_end": null,
"aa_length": 1304,
"cds_start": 3630,
"cds_end": null,
"cds_length": 3915,
"cdna_start": 4010,
"cdna_end": null,
"cdna_length": 4388,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "HM",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant",
"splice_donor_variant",
"splice_region_variant",
"intron_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH6",
"gene_hgnc_id": 7329,
"hgvs_c": "c.3624_3627+9delTATGGTATGTGCA",
"hgvs_p": "p.His1208fs",
"transcript": "NM_001406798.1",
"protein_id": "NP_001393727.1",
"transcript_support_level": null,
"aa_start": 1208,
"aa_end": null,
"aa_length": 1302,
"cds_start": 3624,
"cds_end": null,
"cds_length": 3909,
"cdna_start": 3713,
"cdna_end": null,
"cdna_length": 4091,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "HM",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant",
"splice_donor_variant",
"splice_region_variant",
"intron_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH6",
"gene_hgnc_id": 7329,
"hgvs_c": "c.3501_3504+9delTATGGTATGTGCA",
"hgvs_p": "p.His1167fs",
"transcript": "NM_001406797.1",
"protein_id": "NP_001393726.1",
"transcript_support_level": null,
"aa_start": 1167,
"aa_end": null,
"aa_length": 1261,
"cds_start": 3501,
"cds_end": null,
"cds_length": 3786,
"cdna_start": 3625,
"cdna_end": null,
"cdna_length": 4003,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "HM",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant",
"splice_donor_variant",
"splice_region_variant",
"intron_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH6",
"gene_hgnc_id": 7329,
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],
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"frequency_reference_population": 6.8408065e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.84081e-7,
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"gnomad_exomes_ac": 1,
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"alphamissense_score": null,
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"bayesdelnoaf_score": null,
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"phylop100way_score": 9.492,
"phylop100way_prediction": "Pathogenic",
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"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 16,
"benign_score": 0,
"pathogenic_score": 16,
"criteria": [
"PVS1",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000234420.11",
"gene_symbol": "MSH6",
"hgnc_id": 7329,
"effects": [
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"splice_donor_variant",
"splice_region_variant",
"intron_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.3798_3801+9delTATGGTATGTGCA",
"hgvs_p": "p.His1266fs"
},
{
"score": 9,
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"criteria": [
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],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000682451.1",
"gene_symbol": "FBXO11",
"hgnc_id": 13590,
"effects": [
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],
"inheritance_mode": "AD",
"hgvs_c": "n.4383_4395delCACATACCATATG",
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}
],
"clinvar_disease": "Hereditary cancer-predisposing syndrome,Hereditary nonpolyposis colorectal neoplasms,Lynch syndrome 5,not provided",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:2 LP:3",
"phenotype_combined": "Hereditary cancer-predisposing syndrome|Hereditary nonpolyposis colorectal neoplasms|not provided|Lynch syndrome 5",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}