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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: 3-136340475-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=136340475&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 136340475,
"ref": "T",
"alt": "C",
"effect": "intron_variant",
"transcript": "NM_005862.3",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": 32,
"intron_rank_end": null,
"gene_symbol": "STAG1",
"gene_hgnc_id": 11354,
"hgvs_c": "c.3672+16A>G",
"hgvs_p": null,
"transcript": "NM_005862.3",
"protein_id": "NP_005853.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1258,
"cds_start": null,
"cds_end": null,
"cds_length": 3777,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000383202.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_005862.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": 32,
"intron_rank_end": null,
"gene_symbol": "STAG1",
"gene_hgnc_id": 11354,
"hgvs_c": "c.3672+16A>G",
"hgvs_p": null,
"transcript": "ENST00000383202.7",
"protein_id": "ENSP00000372689.2",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 1258,
"cds_start": null,
"cds_end": null,
"cds_length": 3777,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_005862.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000383202.7"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": 31,
"intron_rank_end": null,
"gene_symbol": "STAG1",
"gene_hgnc_id": 11354,
"hgvs_c": "c.3561+16A>G",
"hgvs_p": null,
"transcript": "ENST00000236698.9",
"protein_id": "ENSP00000236698.5",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 1221,
"cds_start": null,
"cds_end": null,
"cds_length": 3666,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000236698.9"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": 34,
"intron_rank_end": null,
"gene_symbol": "STAG1",
"gene_hgnc_id": 11354,
"hgvs_c": "n.*3662+16A>G",
"hgvs_p": null,
"transcript": "ENST00000483235.5",
"protein_id": "ENSP00000419093.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000483235.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": 32,
"intron_rank_end": null,
"gene_symbol": "STAG1",
"gene_hgnc_id": 11354,
"hgvs_c": "c.3702+16A>G",
"hgvs_p": null,
"transcript": "ENST00000862968.1",
"protein_id": "ENSP00000533027.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1268,
"cds_start": null,
"cds_end": null,
"cds_length": 3807,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000862968.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": 32,
"intron_rank_end": null,
"gene_symbol": "STAG1",
"gene_hgnc_id": 11354,
"hgvs_c": "c.3693+16A>G",
"hgvs_p": null,
"transcript": "ENST00000968454.1",
"protein_id": "ENSP00000638513.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1265,
"cds_start": null,
"cds_end": null,
"cds_length": 3798,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000968454.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": 33,
"intron_rank_end": null,
"gene_symbol": "STAG1",
"gene_hgnc_id": 11354,
"hgvs_c": "c.3672+16A>G",
"hgvs_p": null,
"transcript": "ENST00000862965.1",
"protein_id": "ENSP00000533024.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1258,
"cds_start": null,
"cds_end": null,
"cds_length": 3777,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000862965.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": 33,
"intron_rank_end": null,
"gene_symbol": "STAG1",
"gene_hgnc_id": 11354,
"hgvs_c": "c.3672+16A>G",
"hgvs_p": null,
"transcript": "ENST00000862966.1",
"protein_id": "ENSP00000533025.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1258,
"cds_start": null,
"cds_end": null,
"cds_length": 3777,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000862966.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": 33,
"intron_rank_end": null,
"gene_symbol": "STAG1",
"gene_hgnc_id": 11354,
"hgvs_c": "c.3672+16A>G",
"hgvs_p": null,
"transcript": "ENST00000862969.1",
"protein_id": "ENSP00000533028.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1258,
"cds_start": null,
"cds_end": null,
"cds_length": 3777,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000862969.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": 33,
"intron_rank_end": null,
"gene_symbol": "STAG1",
"gene_hgnc_id": 11354,
"hgvs_c": "c.3672+16A>G",
"hgvs_p": null,
"transcript": "ENST00000968452.1",
"protein_id": "ENSP00000638511.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1258,
"cds_start": null,
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"cds_length": 3777,
"cdna_start": null,
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"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000968452.1"
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
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"exon_count": 35,
"intron_rank": 33,
"intron_rank_end": null,
"gene_symbol": "STAG1",
"gene_hgnc_id": 11354,
"hgvs_c": "c.3672+16A>G",
"hgvs_p": null,
"transcript": "ENST00000968456.1",
"protein_id": "ENSP00000638515.1",
"transcript_support_level": null,
"aa_start": null,
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"cds_start": null,
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"cdna_start": null,
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"mane_select": null,
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"biotype": "protein_coding",
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},
{
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"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
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"exon_count": 33,
"intron_rank": 31,
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"gene_symbol": "STAG1",
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"hgvs_c": "c.3591+16A>G",
"hgvs_p": null,
"transcript": "ENST00000862964.1",
"protein_id": "ENSP00000533023.1",
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"cds_start": null,
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"cdna_start": null,
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"biotype": "protein_coding",
"feature": "ENST00000862964.1"
},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
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"exon_count": 33,
"intron_rank": 31,
"intron_rank_end": null,
"gene_symbol": "STAG1",
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"hgvs_c": "c.3579+16A>G",
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"transcript": "ENST00000862967.1",
"protein_id": "ENSP00000533026.1",
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"cds_start": null,
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"cdna_start": null,
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"biotype": "protein_coding",
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},
{
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"strand": false,
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],
"exon_rank": null,
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"gene_symbol": "STAG1",
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"transcript": "ENST00000968455.1",
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"feature": "ENST00000968455.1"
},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
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"exon_count": 32,
"intron_rank": 30,
"intron_rank_end": null,
"gene_symbol": "STAG1",
"gene_hgnc_id": 11354,
"hgvs_c": "c.3357+16A>G",
"hgvs_p": null,
"transcript": "ENST00000968453.1",
"protein_id": "ENSP00000638512.1",
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"aa_start": null,
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"cds_start": null,
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"cdna_start": null,
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"biotype": "protein_coding",
"feature": "ENST00000968453.1"
},
{
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"protein_coding": true,
"strand": false,
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],
"exon_rank": null,
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"exon_count": 33,
"intron_rank": 31,
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"gene_symbol": "STAG1",
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"hgvs_c": "c.2892+16A>G",
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"transcript": "ENST00000434713.6",
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"biotype": "protein_coding",
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},
{
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"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
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"intron_rank": 33,
"intron_rank_end": null,
"gene_symbol": "STAG1",
"gene_hgnc_id": 11354,
"hgvs_c": "c.*3311+16A>G",
"hgvs_p": null,
"transcript": "ENST00000629124.2",
"protein_id": "ENSP00000486745.1",
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"biotype": "protein_coding",
"feature": "ENST00000629124.2"
},
{
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"protein_coding": true,
"strand": false,
"consequences": [
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],
"exon_rank": null,
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"exon_count": 33,
"intron_rank": 31,
"intron_rank_end": null,
"gene_symbol": "STAG1",
"gene_hgnc_id": 11354,
"hgvs_c": "c.3381+16A>G",
"hgvs_p": null,
"transcript": "XM_047447228.1",
"protein_id": "XP_047303184.1",
"transcript_support_level": null,
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},
{
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],
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"intron_rank_end": null,
"gene_symbol": "STAG1",
"gene_hgnc_id": 11354,
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},
{
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"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
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"intron_rank": 30,
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"gene_symbol": "STAG1",
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},
{
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"strand": false,
"consequences": [
"intron_variant"
],
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"gene_symbol": "STAG1",
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"hgvs_c": "c.3261+16A>G",
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"transcript": "XM_047447231.1",
"protein_id": "XP_047303187.1",
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"mane_select": null,
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"biotype": "protein_coding",
"feature": "XM_047447231.1"
},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": 26,
"intron_rank_end": null,
"gene_symbol": "STAG1",
"gene_hgnc_id": 11354,
"hgvs_c": "c.2994+16A>G",
"hgvs_p": null,
"transcript": "XM_047447235.1",
"protein_id": "XP_047303191.1",
"transcript_support_level": null,
"aa_start": null,
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"cds_start": null,
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"cdna_start": null,
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"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047447235.1"
},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": 20,
"intron_rank_end": null,
"gene_symbol": "STAG1",
"gene_hgnc_id": 11354,
"hgvs_c": "c.2361+16A>G",
"hgvs_p": null,
"transcript": "XM_017005525.2",
"protein_id": "XP_016861014.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 821,
"cds_start": null,
"cds_end": null,
"cds_length": 2466,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017005525.2"
}
],
"gene_symbol": "STAG1",
"gene_hgnc_id": 11354,
"dbsnp": "rs374980869",
"frequency_reference_population": 0.000237822,
"hom_count_reference_population": 0,
"allele_count_reference_population": 361,
"gnomad_exomes_af": 0.000243839,
"gnomad_genomes_af": 0.000183865,
"gnomad_exomes_ac": 333,
"gnomad_genomes_ac": 28,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.8299999833106995,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.83,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.691,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.02,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"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_005862.3",
"gene_symbol": "STAG1",
"hgnc_id": 11354,
"effects": [
"intron_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.3672+16A>G",
"hgvs_p": null
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:2",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}