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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: 2-47480871-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=47480871&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 47480871,
"ref": "G",
"alt": "A",
"effect": "splice_region_variant,synonymous_variant",
"transcript": "ENST00000233146.7",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH2",
"gene_hgnc_id": 7325,
"hgvs_c": "c.2634G>A",
"hgvs_p": "p.Glu878Glu",
"transcript": "NM_000251.3",
"protein_id": "NP_000242.1",
"transcript_support_level": null,
"aa_start": 878,
"aa_end": null,
"aa_length": 934,
"cds_start": 2634,
"cds_end": null,
"cds_length": 2805,
"cdna_start": 2670,
"cdna_end": null,
"cdna_length": 3115,
"mane_select": "ENST00000233146.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH2",
"gene_hgnc_id": 7325,
"hgvs_c": "c.2634G>A",
"hgvs_p": "p.Glu878Glu",
"transcript": "ENST00000233146.7",
"protein_id": "ENSP00000233146.2",
"transcript_support_level": 1,
"aa_start": 878,
"aa_end": null,
"aa_length": 934,
"cds_start": 2634,
"cds_end": null,
"cds_length": 2805,
"cdna_start": 2670,
"cdna_end": null,
"cdna_length": 3115,
"mane_select": "NM_000251.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH2",
"gene_hgnc_id": 7325,
"hgvs_c": "c.2634G>A",
"hgvs_p": "p.Glu878Glu",
"transcript": "ENST00000406134.5",
"protein_id": "ENSP00000384199.1",
"transcript_support_level": 1,
"aa_start": 878,
"aa_end": null,
"aa_length": 921,
"cds_start": 2634,
"cds_end": null,
"cds_length": 2766,
"cdna_start": 2696,
"cdna_end": null,
"cdna_length": 3628,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH2",
"gene_hgnc_id": 7325,
"hgvs_c": "c.2634G>A",
"hgvs_p": "p.Glu878Glu",
"transcript": "NM_001406674.1",
"protein_id": "NP_001393603.1",
"transcript_support_level": null,
"aa_start": 878,
"aa_end": null,
"aa_length": 1014,
"cds_start": 2634,
"cds_end": null,
"cds_length": 3045,
"cdna_start": 2670,
"cdna_end": null,
"cdna_length": 5813,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH2",
"gene_hgnc_id": 7325,
"hgvs_c": "c.2634G>A",
"hgvs_p": "p.Glu878Glu",
"transcript": "NM_001406631.1",
"protein_id": "NP_001393560.1",
"transcript_support_level": null,
"aa_start": 878,
"aa_end": null,
"aa_length": 979,
"cds_start": 2634,
"cds_end": null,
"cds_length": 2940,
"cdna_start": 2670,
"cdna_end": null,
"cdna_length": 3210,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH2",
"gene_hgnc_id": 7325,
"hgvs_c": "c.2634G>A",
"hgvs_p": "p.Glu878Glu",
"transcript": "NM_001406632.1",
"protein_id": "NP_001393561.1",
"transcript_support_level": null,
"aa_start": 878,
"aa_end": null,
"aa_length": 976,
"cds_start": 2634,
"cds_end": null,
"cds_length": 2931,
"cdna_start": 2670,
"cdna_end": null,
"cdna_length": 3284,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH2",
"gene_hgnc_id": 7325,
"hgvs_c": "c.2634G>A",
"hgvs_p": "p.Glu878Glu",
"transcript": "NM_001406633.1",
"protein_id": "NP_001393562.1",
"transcript_support_level": null,
"aa_start": 878,
"aa_end": null,
"aa_length": 975,
"cds_start": 2634,
"cds_end": null,
"cds_length": 2928,
"cdna_start": 2670,
"cdna_end": null,
"cdna_length": 3134,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH2",
"gene_hgnc_id": 7325,
"hgvs_c": "c.2634G>A",
"hgvs_p": "p.Glu878Glu",
"transcript": "NM_001406634.1",
"protein_id": "NP_001393563.1",
"transcript_support_level": null,
"aa_start": 878,
"aa_end": null,
"aa_length": 974,
"cds_start": 2634,
"cds_end": null,
"cds_length": 2925,
"cdna_start": 2670,
"cdna_end": null,
"cdna_length": 5693,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH2",
"gene_hgnc_id": 7325,
"hgvs_c": "c.2634G>A",
"hgvs_p": "p.Glu878Glu",
"transcript": "NM_001406635.1",
"protein_id": "NP_001393564.1",
"transcript_support_level": null,
"aa_start": 878,
"aa_end": null,
"aa_length": 969,
"cds_start": 2634,
"cds_end": null,
"cds_length": 2910,
"cdna_start": 2670,
"cdna_end": null,
"cdna_length": 3051,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH2",
"gene_hgnc_id": 7325,
"hgvs_c": "c.2601G>A",
"hgvs_p": "p.Glu867Glu",
"transcript": "NM_001406636.1",
"protein_id": "NP_001393565.1",
"transcript_support_level": null,
"aa_start": 867,
"aa_end": null,
"aa_length": 958,
"cds_start": 2601,
"cds_end": null,
"cds_length": 2877,
"cdna_start": 2637,
"cdna_end": null,
"cdna_length": 3018,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH2",
"gene_hgnc_id": 7325,
"hgvs_c": "c.2634G>A",
"hgvs_p": "p.Glu878Glu",
"transcript": "NM_001406637.1",
"protein_id": "NP_001393566.1",
"transcript_support_level": null,
"aa_start": 878,
"aa_end": null,
"aa_length": 957,
"cds_start": 2634,
"cds_end": null,
"cds_length": 2874,
"cdna_start": 2670,
"cdna_end": null,
"cdna_length": 4436,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH2",
"gene_hgnc_id": 7325,
"hgvs_c": "c.2673G>A",
"hgvs_p": "p.Glu891Glu",
"transcript": "NM_001406638.1",
"protein_id": "NP_001393567.1",
"transcript_support_level": null,
"aa_start": 891,
"aa_end": null,
"aa_length": 947,
"cds_start": 2673,
"cds_end": null,
"cds_length": 2844,
"cdna_start": 2709,
"cdna_end": null,
"cdna_length": 10637,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH2",
"gene_hgnc_id": 7325,
"hgvs_c": "c.2634G>A",
"hgvs_p": "p.Glu878Glu",
"transcript": "NM_001406639.1",
"protein_id": "NP_001393568.1",
"transcript_support_level": null,
"aa_start": 878,
"aa_end": null,
"aa_length": 945,
"cds_start": 2634,
"cds_end": null,
"cds_length": 2838,
"cdna_start": 2670,
"cdna_end": null,
"cdna_length": 3191,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH2",
"gene_hgnc_id": 7325,
"hgvs_c": "c.2634G>A",
"hgvs_p": "p.Glu878Glu",
"transcript": "NM_001406640.1",
"protein_id": "NP_001393569.1",
"transcript_support_level": null,
"aa_start": 878,
"aa_end": null,
"aa_length": 945,
"cds_start": 2634,
"cds_end": null,
"cds_length": 2838,
"cdna_start": 2670,
"cdna_end": null,
"cdna_length": 3032,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH2",
"gene_hgnc_id": 7325,
"hgvs_c": "c.2634G>A",
"hgvs_p": "p.Glu878Glu",
"transcript": "NM_001406641.1",
"protein_id": "NP_001393570.1",
"transcript_support_level": null,
"aa_start": 878,
"aa_end": null,
"aa_length": 934,
"cds_start": 2634,
"cds_end": null,
"cds_length": 2805,
"cdna_start": 2670,
"cdna_end": null,
"cdna_length": 10598,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH2",
"gene_hgnc_id": 7325,
"hgvs_c": "c.2634G>A",
"hgvs_p": "p.Glu878Glu",
"transcript": "NM_001406642.1",
"protein_id": "NP_001393571.1",
"transcript_support_level": null,
"aa_start": 878,
"aa_end": null,
"aa_length": 929,
"cds_start": 2634,
"cds_end": null,
"cds_length": 2790,
"cdna_start": 2670,
"cdna_end": null,
"cdna_length": 2909,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH2",
"gene_hgnc_id": 7325,
"hgvs_c": "c.2634G>A",
"hgvs_p": "p.Glu878Glu",
"transcript": "NM_001406643.1",
"protein_id": "NP_001393572.1",
"transcript_support_level": null,
"aa_start": 878,
"aa_end": null,
"aa_length": 926,
"cds_start": 2634,
"cds_end": null,
"cds_length": 2781,
"cdna_start": 2670,
"cdna_end": null,
"cdna_length": 3626,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH2",
"gene_hgnc_id": 7325,
"hgvs_c": "c.2634G>A",
"hgvs_p": "p.Glu878Glu",
"transcript": "NM_001406644.1",
"protein_id": "NP_001393573.1",
"transcript_support_level": null,
"aa_start": 878,
"aa_end": null,
"aa_length": 924,
"cds_start": 2634,
"cds_end": null,
"cds_length": 2775,
"cdna_start": 2670,
"cdna_end": null,
"cdna_length": 5585,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH2",
"gene_hgnc_id": 7325,
"hgvs_c": "c.2634G>A",
"hgvs_p": "p.Glu878Glu",
"transcript": "ENST00000645506.1",
"protein_id": "ENSP00000495455.1",
"transcript_support_level": null,
"aa_start": 878,
"aa_end": null,
"aa_length": 924,
"cds_start": 2634,
"cds_end": null,
"cds_length": 2775,
"cdna_start": 2707,
"cdna_end": null,
"cdna_length": 7893,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH2",
"gene_hgnc_id": 7325,
"hgvs_c": "c.2634G>A",
"hgvs_p": "p.Glu878Glu",
"transcript": "NM_001406645.1",
"protein_id": "NP_001393574.1",
"transcript_support_level": null,
"aa_start": 878,
"aa_end": null,
"aa_length": 921,
"cds_start": 2634,
"cds_end": null,
"cds_length": 2766,
"cdna_start": 2670,
"cdna_end": null,
"cdna_length": 10404,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH2",
"gene_hgnc_id": 7325,
"hgvs_c": "c.2634G>A",
"hgvs_p": "p.Glu878Glu",
"transcript": "NM_001406646.1",
"protein_id": "NP_001393575.1",
"transcript_support_level": null,
"aa_start": 878,
"aa_end": null,
"aa_length": 918,
"cds_start": 2634,
"cds_end": null,
"cds_length": 2757,
"cdna_start": 2670,
"cdna_end": null,
"cdna_length": 4488,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH2",
"gene_hgnc_id": 7325,
"hgvs_c": "c.2484G>A",
"hgvs_p": "p.Glu828Glu",
"transcript": "NM_001406647.1",
"protein_id": "NP_001393576.1",
"transcript_support_level": null,
"aa_start": 828,
"aa_end": null,
"aa_length": 903,
"cds_start": 2484,
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"hgvs_c": "n.*487G>A",
"hgvs_p": null,
"transcript": "ENST00000713867.1",
"protein_id": "ENSP00000519172.1",
"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": 3443,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "MSH2",
"gene_hgnc_id": 7325,
"dbsnp": "rs63751624",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.2199999988079071,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 1,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.22,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 8.654,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.61,
"spliceai_max_prediction": "Pathogenic",
"dbscsnv_ada_score": 0.999973991689275,
"dbscsnv_ada_prediction": "Pathogenic",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 14,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM2,PP3_Strong,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 14,
"benign_score": 0,
"pathogenic_score": 14,
"criteria": [
"PM2",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000233146.7",
"gene_symbol": "MSH2",
"hgnc_id": 7325,
"effects": [
"splice_region_variant",
"synonymous_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.2634G>A",
"hgvs_p": "p.Glu878Glu"
}
],
"clinvar_disease": "Hereditary cancer-predisposing syndrome,Hereditary nonpolyposis colon cancer,Hereditary nonpolyposis colorectal neoplasms,Lynch syndrome,Lynch syndrome 1,not provided",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "reviewed by expert panel",
"clinvar_submissions_summary": "P:5 LP:1",
"phenotype_combined": "Lynch syndrome|Hereditary cancer-predisposing syndrome|not provided|Hereditary nonpolyposis colorectal neoplasms|Hereditary nonpolyposis colon cancer|Lynch syndrome 1",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}