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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: 3-136473546-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=136473546&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM2",
"PP3_Moderate",
"PP5_Very_Strong"
],
"effects": [
"missense_variant"
],
"gene_symbol": "STAG1",
"hgnc_id": 11354,
"hgvs_c": "c.1118G>A",
"hgvs_p": "p.Arg373Gln",
"inheritance_mode": "AD",
"pathogenic_score": 12,
"score": 12,
"transcript": "NM_005862.3",
"verdict": "Pathogenic"
}
],
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM2,PP3_Moderate,PP5_Very_Strong",
"acmg_score": 12,
"allele_count_reference_population": 0,
"alphamissense_prediction": null,
"alphamissense_score": 0.9985,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.18,
"chr": "3",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_disease": " autosomal dominant 47,Inborn genetic diseases,Intellectual disability,STAG1-related disorder,not provided",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:2 LP:2",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.8409621715545654,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 1258,
"aa_ref": "R",
"aa_start": 373,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6062,
"cdna_start": 1385,
"cds_end": null,
"cds_length": 3777,
"cds_start": 1118,
"consequences": [
"missense_variant"
],
"exon_count": 34,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "NM_005862.3",
"gene_hgnc_id": 11354,
"gene_symbol": "STAG1",
"hgvs_c": "c.1118G>A",
"hgvs_p": "p.Arg373Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000383202.7",
"protein_coding": true,
"protein_id": "NP_005853.2",
"strand": false,
"transcript": "NM_005862.3",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 1258,
"aa_ref": "R",
"aa_start": 373,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 6062,
"cdna_start": 1385,
"cds_end": null,
"cds_length": 3777,
"cds_start": 1118,
"consequences": [
"missense_variant"
],
"exon_count": 34,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000383202.7",
"gene_hgnc_id": 11354,
"gene_symbol": "STAG1",
"hgvs_c": "c.1118G>A",
"hgvs_p": "p.Arg373Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_005862.3",
"protein_coding": true,
"protein_id": "ENSP00000372689.2",
"strand": false,
"transcript": "ENST00000383202.7",
"transcript_support_level": 1
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 1221,
"aa_ref": "R",
"aa_start": 373,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5951,
"cdna_start": 1385,
"cds_end": null,
"cds_length": 3666,
"cds_start": 1118,
"consequences": [
"missense_variant"
],
"exon_count": 33,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000236698.9",
"gene_hgnc_id": 11354,
"gene_symbol": "STAG1",
"hgvs_c": "c.1118G>A",
"hgvs_p": "p.Arg373Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000236698.5",
"strand": false,
"transcript": "ENST00000236698.9",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 5206,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 36,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "ENST00000483235.5",
"gene_hgnc_id": 11354,
"gene_symbol": "STAG1",
"hgvs_c": "n.*1210G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000419093.1",
"strand": false,
"transcript": "ENST00000483235.5",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 2914,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 22,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000487065.5",
"gene_hgnc_id": 11354,
"gene_symbol": "STAG1",
"hgvs_c": "n.*757G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000418472.1",
"strand": false,
"transcript": "ENST00000487065.5",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 5206,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 36,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "ENST00000483235.5",
"gene_hgnc_id": 11354,
"gene_symbol": "STAG1",
"hgvs_c": "n.*1210G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000419093.1",
"strand": false,
"transcript": "ENST00000483235.5",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 2914,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 22,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000487065.5",
"gene_hgnc_id": 11354,
"gene_symbol": "STAG1",
"hgvs_c": "n.*757G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000418472.1",
"strand": false,
"transcript": "ENST00000487065.5",
"transcript_support_level": 1
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 1268,
"aa_ref": "R",
"aa_start": 373,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6089,
"cdna_start": 1385,
"cds_end": null,
"cds_length": 3807,
"cds_start": 1118,
"consequences": [
"missense_variant"
],
"exon_count": 34,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000862968.1",
"gene_hgnc_id": 11354,
"gene_symbol": "STAG1",
"hgvs_c": "c.1118G>A",
"hgvs_p": "p.Arg373Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000533027.1",
"strand": false,
"transcript": "ENST00000862968.1",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 1265,
"aa_ref": "R",
"aa_start": 373,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6081,
"cdna_start": 1381,
"cds_end": null,
"cds_length": 3798,
"cds_start": 1118,
"consequences": [
"missense_variant"
],
"exon_count": 34,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000968454.1",
"gene_hgnc_id": 11354,
"gene_symbol": "STAG1",
"hgvs_c": "c.1118G>A",
"hgvs_p": "p.Arg373Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000638513.1",
"strand": false,
"transcript": "ENST00000968454.1",
"transcript_support_level": null
},
{
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"aa_length": 1258,
"aa_ref": "R",
"aa_start": 373,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6155,
"cdna_start": 1478,
"cds_end": null,
"cds_length": 3777,
"cds_start": 1118,
"consequences": [
"missense_variant"
],
"exon_count": 35,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000862965.1",
"gene_hgnc_id": 11354,
"gene_symbol": "STAG1",
"hgvs_c": "c.1118G>A",
"hgvs_p": "p.Arg373Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000533024.1",
"strand": false,
"transcript": "ENST00000862965.1",
"transcript_support_level": null
},
{
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"aa_length": 1258,
"aa_ref": "R",
"aa_start": 373,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6184,
"cdna_start": 1507,
"cds_end": null,
"cds_length": 3777,
"cds_start": 1118,
"consequences": [
"missense_variant"
],
"exon_count": 35,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000862966.1",
"gene_hgnc_id": 11354,
"gene_symbol": "STAG1",
"hgvs_c": "c.1118G>A",
"hgvs_p": "p.Arg373Gln",
"intron_rank": null,
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"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000533025.1",
"strand": false,
"transcript": "ENST00000862966.1",
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},
{
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"aa_length": 1258,
"aa_ref": "R",
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"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5098,
"cdna_start": 1583,
"cds_end": null,
"cds_length": 3777,
"cds_start": 1118,
"consequences": [
"missense_variant"
],
"exon_count": 35,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000862969.1",
"gene_hgnc_id": 11354,
"gene_symbol": "STAG1",
"hgvs_c": "c.1118G>A",
"hgvs_p": "p.Arg373Gln",
"intron_rank": null,
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"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000533028.1",
"strand": false,
"transcript": "ENST00000862969.1",
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},
{
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"biotype": "protein_coding",
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"cdna_start": 1505,
"cds_end": null,
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"consequences": [
"missense_variant"
],
"exon_count": 35,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000968452.1",
"gene_hgnc_id": 11354,
"gene_symbol": "STAG1",
"hgvs_c": "c.1118G>A",
"hgvs_p": "p.Arg373Gln",
"intron_rank": null,
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"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000638511.1",
"strand": false,
"transcript": "ENST00000968452.1",
"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": 4959,
"cdna_start": 1454,
"cds_end": null,
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"consequences": [
"missense_variant"
],
"exon_count": 35,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000968456.1",
"gene_hgnc_id": 11354,
"gene_symbol": "STAG1",
"hgvs_c": "c.1118G>A",
"hgvs_p": "p.Arg373Gln",
"intron_rank": null,
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"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000638515.1",
"strand": false,
"transcript": "ENST00000968456.1",
"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": 6032,
"cdna_start": 1439,
"cds_end": null,
"cds_length": 3696,
"cds_start": 1118,
"consequences": [
"missense_variant"
],
"exon_count": 33,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000862964.1",
"gene_hgnc_id": 11354,
"gene_symbol": "STAG1",
"hgvs_c": "c.1118G>A",
"hgvs_p": "p.Arg373Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000533023.1",
"strand": false,
"transcript": "ENST00000862964.1",
"transcript_support_level": null
},
{
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"aa_length": 1227,
"aa_ref": "R",
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"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5966,
"cdna_start": 1382,
"cds_end": null,
"cds_length": 3684,
"cds_start": 1118,
"consequences": [
"missense_variant"
],
"exon_count": 33,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000862967.1",
"gene_hgnc_id": 11354,
"gene_symbol": "STAG1",
"hgvs_c": "c.1118G>A",
"hgvs_p": "p.Arg373Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000533026.1",
"strand": false,
"transcript": "ENST00000862967.1",
"transcript_support_level": null
},
{
"aa_alt": "Q",
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"aa_length": 1190,
"aa_ref": "R",
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"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4685,
"cdna_start": 1384,
"cds_end": null,
"cds_length": 3573,
"cds_start": 1118,
"consequences": [
"missense_variant"
],
"exon_count": 33,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000968455.1",
"gene_hgnc_id": 11354,
"gene_symbol": "STAG1",
"hgvs_c": "c.1118G>A",
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"intron_rank": null,
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"mane_plus": null,
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"protein_coding": true,
"protein_id": "ENSP00000638514.1",
"strand": false,
"transcript": "ENST00000968455.1",
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},
{
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"aa_ref": "R",
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"biotype": "protein_coding",
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"cdna_start": 1385,
"cds_end": null,
"cds_length": 3462,
"cds_start": 1118,
"consequences": [
"missense_variant"
],
"exon_count": 32,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000968453.1",
"gene_hgnc_id": 11354,
"gene_symbol": "STAG1",
"hgvs_c": "c.1118G>A",
"hgvs_p": "p.Arg373Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000638512.1",
"strand": false,
"transcript": "ENST00000968453.1",
"transcript_support_level": null
},
{
"aa_alt": "Q",
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"aa_ref": "R",
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"biotype": "protein_coding",
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"cdna_end": null,
"cdna_length": 5064,
"cdna_start": 1410,
"cds_end": null,
"cds_length": 2997,
"cds_start": 440,
"consequences": [
"missense_variant"
],
"exon_count": 33,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000434713.6",
"gene_hgnc_id": 11354,
"gene_symbol": "STAG1",
"hgvs_c": "c.440G>A",
"hgvs_p": "p.Arg147Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000404396.2",
"strand": false,
"transcript": "ENST00000434713.6",
"transcript_support_level": 5
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 188,
"aa_ref": "R",
"aa_start": 19,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 570,
"cdna_start": 58,
"cds_end": null,
"cds_length": 568,
"cds_start": 56,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000492318.1",
"gene_hgnc_id": 11354,
"gene_symbol": "STAG1",
"hgvs_c": "c.56G>A",
"hgvs_p": "p.Arg19Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000419317.1",
"strand": false,
"transcript": "ENST00000492318.1",
"transcript_support_level": 5
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 1161,
"aa_ref": "R",
"aa_start": 276,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5833,
"cdna_start": 1156,
"cds_end": null,
"cds_length": 3486,
"cds_start": 827,
"consequences": [
"missense_variant"
],
"exon_count": 33,
"exon_rank": 10,
"exon_rank_end": null,
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