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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: 2-172469112-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=172469112&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 172469112,
"ref": "C",
"alt": "A",
"effect": "intron_variant",
"transcript": "ENST00000684293.1",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "ITGA6",
"gene_hgnc_id": 6142,
"hgvs_c": "c.388-13C>A",
"hgvs_p": null,
"transcript": "NM_001394928.1",
"protein_id": "NP_001381857.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1130,
"cds_start": -4,
"cds_end": null,
"cds_length": 3393,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5803,
"mane_select": null,
"mane_plus": "ENST00000442250.6",
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "ITGA6",
"gene_hgnc_id": 6142,
"hgvs_c": "c.388-13C>A",
"hgvs_p": null,
"transcript": "ENST00000442250.6",
"protein_id": "ENSP00000406694.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 1130,
"cds_start": -4,
"cds_end": null,
"cds_length": 3393,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5803,
"mane_select": null,
"mane_plus": "NM_001394928.1",
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "ITGA6",
"gene_hgnc_id": 6142,
"hgvs_c": "c.388-13C>A",
"hgvs_p": null,
"transcript": "NM_000210.4",
"protein_id": "NP_000201.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1073,
"cds_start": -4,
"cds_end": null,
"cds_length": 3222,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5816,
"mane_select": "ENST00000684293.1",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "ITGA6",
"gene_hgnc_id": 6142,
"hgvs_c": "c.388-13C>A",
"hgvs_p": null,
"transcript": "ENST00000684293.1",
"protein_id": "ENSP00000508249.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1073,
"cds_start": -4,
"cds_end": null,
"cds_length": 3222,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5816,
"mane_select": "NM_000210.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "ITGA6",
"gene_hgnc_id": 6142,
"hgvs_c": "c.388-13C>A",
"hgvs_p": null,
"transcript": "ENST00000264107.12",
"protein_id": "ENSP00000264107.8",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 1058,
"cds_start": -4,
"cds_end": null,
"cds_length": 3177,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5488,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "ITGA6",
"gene_hgnc_id": 6142,
"hgvs_c": "c.46-13C>A",
"hgvs_p": null,
"transcript": "ENST00000412899.5",
"protein_id": "ENSP00000413470.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 230,
"cds_start": -4,
"cds_end": null,
"cds_length": 693,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 970,
"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": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGA6",
"gene_hgnc_id": 6142,
"hgvs_c": "n.115C>A",
"hgvs_p": null,
"transcript": "ENST00000497107.1",
"protein_id": null,
"transcript_support_level": 2,
"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": 573,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "ITGA6",
"gene_hgnc_id": 6142,
"hgvs_c": "c.388-13C>A",
"hgvs_p": null,
"transcript": "NM_001079818.3",
"protein_id": "NP_001073286.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1091,
"cds_start": -4,
"cds_end": null,
"cds_length": 3276,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5686,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "ITGA6",
"gene_hgnc_id": 6142,
"hgvs_c": "c.388-13C>A",
"hgvs_p": null,
"transcript": "ENST00000409080.6",
"protein_id": "ENSP00000386896.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 1091,
"cds_start": -4,
"cds_end": null,
"cds_length": 3276,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5686,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "ITGA6",
"gene_hgnc_id": 6142,
"hgvs_c": "c.388-13C>A",
"hgvs_p": null,
"transcript": "ENST00000458358.5",
"protein_id": "ENSP00000394169.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 1086,
"cds_start": -4,
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"cds_length": 3261,
"cdna_start": null,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "ITGA6",
"gene_hgnc_id": 6142,
"hgvs_c": "c.388-13C>A",
"hgvs_p": null,
"transcript": "NM_001365529.2",
"protein_id": "NP_001352458.1",
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"aa_start": null,
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"cds_start": -4,
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"cdna_start": null,
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"feature": null
},
{
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"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
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"exon_count": 26,
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"gene_symbol": "ITGA6",
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"hgvs_c": "c.388-13C>A",
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"transcript": "NM_001365530.2",
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},
{
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"strand": true,
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],
"exon_rank": null,
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"exon_count": 28,
"intron_rank": 6,
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"gene_symbol": "ITGA6",
"gene_hgnc_id": 6142,
"hgvs_c": "c.46-13C>A",
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"transcript": "ENST00000715295.1",
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},
{
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"strand": true,
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],
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"intron_rank": 3,
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"gene_symbol": "ITGA6",
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"hgvs_c": "c.46-13C>A",
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"transcript": "NM_001316306.2",
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},
{
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],
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"intron_rank": 3,
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"gene_symbol": "ITGA6",
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"hgvs_c": "c.46-13C>A",
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"transcript": "ENST00000409532.5",
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},
{
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"strand": false,
"consequences": [
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],
"exon_rank": null,
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"exon_count": 4,
"intron_rank": 3,
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"gene_symbol": "ITGA6-AS1",
"gene_hgnc_id": 40308,
"hgvs_c": "n.533-4538G>T",
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"transcript": "ENST00000715602.2",
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},
{
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],
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"gene_symbol": "ITGA6-AS1",
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"hgvs_c": "n.268-4538G>T",
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"transcript": "ENST00000830320.1",
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},
{
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"strand": false,
"consequences": [
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],
"exon_rank": null,
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"intron_rank": 2,
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"gene_symbol": "PDK1-AS1",
"gene_hgnc_id": 40441,
"hgvs_c": "n.519-4538G>T",
"hgvs_p": null,
"transcript": "NR_199651.1",
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},
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"strand": false,
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],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "PDK1-AS1",
"gene_hgnc_id": 40441,
"hgvs_c": "n.704-4538G>T",
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},
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],
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},
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],
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"gene_symbol": "PDK1-AS1",
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},
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"consequences": [
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],
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"exon_count": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "PDK1-AS1",
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"hgvs_c": "n.704-3091G>T",
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"transcript": "NR_199655.1",
"protein_id": null,
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"feature": null
},
{
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"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "PDK1-AS1",
"gene_hgnc_id": 40441,
"hgvs_c": "n.704-3091G>T",
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"transcript": "NR_199656.1",
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},
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],
"gene_symbol": "ITGA6",
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"computational_score_selected": -0.7400000095367432,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.05000000074505806,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
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"alphamissense_score": null,
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"bayesdelnoaf_score": -0.74,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.079,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.05,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": null,
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"mitotip_score": null,
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"acmg_score": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BA1",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000684293.1",
"gene_symbol": "ITGA6",
"hgnc_id": 6142,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.388-13C>A",
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},
{
"score": -20,
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"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "NR_199651.1",
"gene_symbol": "PDK1-AS1",
"hgnc_id": 40441,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.519-4538G>T",
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},
{
"score": -20,
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"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000715602.2",
"gene_symbol": "ITGA6-AS1",
"hgnc_id": 40308,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.533-4538G>T",
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}
],
"clinvar_disease": "Junctional epidermolysis bullosa with pyloric atresia,not provided",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:4",
"phenotype_combined": "Junctional epidermolysis bullosa with pyloric atresia|not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}