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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: 13-108208700-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=13&pos=108208700&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "13",
"pos": 108208700,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000442234.6",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIG4",
"gene_hgnc_id": 6601,
"hgvs_c": "c.2569G>A",
"hgvs_p": "p.Ala857Thr",
"transcript": "NM_206937.2",
"protein_id": "NP_996820.1",
"transcript_support_level": null,
"aa_start": 857,
"aa_end": null,
"aa_length": 911,
"cds_start": 2569,
"cds_end": null,
"cds_length": 2736,
"cdna_start": 2723,
"cdna_end": null,
"cdna_length": 3981,
"mane_select": "ENST00000442234.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIG4",
"gene_hgnc_id": 6601,
"hgvs_c": "c.2569G>A",
"hgvs_p": "p.Ala857Thr",
"transcript": "ENST00000442234.6",
"protein_id": "ENSP00000402030.1",
"transcript_support_level": 1,
"aa_start": 857,
"aa_end": null,
"aa_length": 911,
"cds_start": 2569,
"cds_end": null,
"cds_length": 2736,
"cdna_start": 2723,
"cdna_end": null,
"cdna_length": 3981,
"mane_select": "NM_206937.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIG4",
"gene_hgnc_id": 6601,
"hgvs_c": "c.2569G>A",
"hgvs_p": "p.Ala857Thr",
"transcript": "ENST00000405925.2",
"protein_id": "ENSP00000385955.1",
"transcript_support_level": 1,
"aa_start": 857,
"aa_end": null,
"aa_length": 911,
"cds_start": 2569,
"cds_end": null,
"cds_length": 2736,
"cdna_start": 2804,
"cdna_end": null,
"cdna_length": 4065,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIG4",
"gene_hgnc_id": 6601,
"hgvs_c": "c.2605G>A",
"hgvs_p": "p.Ala869Thr",
"transcript": "NM_001352604.2",
"protein_id": "NP_001339533.1",
"transcript_support_level": null,
"aa_start": 869,
"aa_end": null,
"aa_length": 923,
"cds_start": 2605,
"cds_end": null,
"cds_length": 2772,
"cdna_start": 2747,
"cdna_end": null,
"cdna_length": 4005,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIG4",
"gene_hgnc_id": 6601,
"hgvs_c": "c.2569G>A",
"hgvs_p": "p.Ala857Thr",
"transcript": "NM_001098268.2",
"protein_id": "NP_001091738.1",
"transcript_support_level": null,
"aa_start": 857,
"aa_end": null,
"aa_length": 911,
"cds_start": 2569,
"cds_end": null,
"cds_length": 2736,
"cdna_start": 2785,
"cdna_end": null,
"cdna_length": 4043,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIG4",
"gene_hgnc_id": 6601,
"hgvs_c": "c.2569G>A",
"hgvs_p": "p.Ala857Thr",
"transcript": "NM_001352598.2",
"protein_id": "NP_001339527.1",
"transcript_support_level": null,
"aa_start": 857,
"aa_end": null,
"aa_length": 911,
"cds_start": 2569,
"cds_end": null,
"cds_length": 2736,
"cdna_start": 3202,
"cdna_end": null,
"cdna_length": 4460,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIG4",
"gene_hgnc_id": 6601,
"hgvs_c": "c.2569G>A",
"hgvs_p": "p.Ala857Thr",
"transcript": "NM_001352599.2",
"protein_id": "NP_001339528.1",
"transcript_support_level": null,
"aa_start": 857,
"aa_end": null,
"aa_length": 911,
"cds_start": 2569,
"cds_end": null,
"cds_length": 2736,
"cdna_start": 3226,
"cdna_end": null,
"cdna_length": 4484,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIG4",
"gene_hgnc_id": 6601,
"hgvs_c": "c.2569G>A",
"hgvs_p": "p.Ala857Thr",
"transcript": "NM_001352600.2",
"protein_id": "NP_001339529.1",
"transcript_support_level": null,
"aa_start": 857,
"aa_end": null,
"aa_length": 911,
"cds_start": 2569,
"cds_end": null,
"cds_length": 2736,
"cdna_start": 3118,
"cdna_end": null,
"cdna_length": 4376,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIG4",
"gene_hgnc_id": 6601,
"hgvs_c": "c.2569G>A",
"hgvs_p": "p.Ala857Thr",
"transcript": "NM_001352601.2",
"protein_id": "NP_001339530.1",
"transcript_support_level": null,
"aa_start": 857,
"aa_end": null,
"aa_length": 911,
"cds_start": 2569,
"cds_end": null,
"cds_length": 2736,
"cdna_start": 2827,
"cdna_end": null,
"cdna_length": 4085,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIG4",
"gene_hgnc_id": 6601,
"hgvs_c": "c.2569G>A",
"hgvs_p": "p.Ala857Thr",
"transcript": "NM_001352602.2",
"protein_id": "NP_001339531.1",
"transcript_support_level": null,
"aa_start": 857,
"aa_end": null,
"aa_length": 911,
"cds_start": 2569,
"cds_end": null,
"cds_length": 2736,
"cdna_start": 2719,
"cdna_end": null,
"cdna_length": 3977,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIG4",
"gene_hgnc_id": 6601,
"hgvs_c": "c.2569G>A",
"hgvs_p": "p.Ala857Thr",
"transcript": "NM_001352603.1",
"protein_id": "NP_001339532.1",
"transcript_support_level": null,
"aa_start": 857,
"aa_end": null,
"aa_length": 911,
"cds_start": 2569,
"cds_end": null,
"cds_length": 2736,
"cdna_start": 2697,
"cdna_end": null,
"cdna_length": 3955,
"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
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"gene_symbol": "LIG4",
"gene_hgnc_id": 6601,
"hgvs_c": "c.2569G>A",
"hgvs_p": "p.Ala857Thr",
"transcript": "NM_001379095.1",
"protein_id": "NP_001366024.1",
"transcript_support_level": null,
"aa_start": 857,
"aa_end": null,
"aa_length": 911,
"cds_start": 2569,
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"cdna_start": 2920,
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"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIG4",
"gene_hgnc_id": 6601,
"hgvs_c": "c.2569G>A",
"hgvs_p": "p.Ala857Thr",
"transcript": "NM_002312.3",
"protein_id": "NP_002303.2",
"transcript_support_level": null,
"aa_start": 857,
"aa_end": null,
"aa_length": 911,
"cds_start": 2569,
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"cdna_start": 2842,
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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": false,
"consequences": [
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],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
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"gene_symbol": "LIG4",
"gene_hgnc_id": 6601,
"hgvs_c": "c.2569G>A",
"hgvs_p": "p.Ala857Thr",
"transcript": "ENST00000611712.4",
"protein_id": "ENSP00000484288.1",
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"feature": null
},
{
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"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
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"gene_symbol": "LIG4",
"gene_hgnc_id": 6601,
"hgvs_c": "c.2569G>A",
"hgvs_p": "p.Ala857Thr",
"transcript": "ENST00000685338.1",
"protein_id": "ENSP00000510567.1",
"transcript_support_level": null,
"aa_start": 857,
"aa_end": null,
"aa_length": 911,
"cds_start": 2569,
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"cdna_start": 2935,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
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"protein_coding": true,
"strand": false,
"consequences": [
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],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
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"gene_symbol": "LIG4",
"gene_hgnc_id": 6601,
"hgvs_c": "c.2569G>A",
"hgvs_p": "p.Ala857Thr",
"transcript": "ENST00000686095.1",
"protein_id": "ENSP00000509942.1",
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"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
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],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIG4",
"gene_hgnc_id": 6601,
"hgvs_c": "c.2569G>A",
"hgvs_p": "p.Ala857Thr",
"transcript": "ENST00000686204.1",
"protein_id": "ENSP00000509685.1",
"transcript_support_level": null,
"aa_start": 857,
"aa_end": null,
"aa_length": 911,
"cds_start": 2569,
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"cdna_start": 5620,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": "A",
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
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],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIG4",
"gene_hgnc_id": 6601,
"hgvs_c": "c.2569G>A",
"hgvs_p": "p.Ala857Thr",
"transcript": "ENST00000686913.1",
"protein_id": "ENSP00000509299.1",
"transcript_support_level": null,
"aa_start": 857,
"aa_end": null,
"aa_length": 911,
"cds_start": 2569,
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"cdna_start": 2911,
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"feature": null
},
{
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"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
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"exon_count": 2,
"intron_rank": null,
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"gene_symbol": "LIG4",
"gene_hgnc_id": 6601,
"hgvs_c": "c.2569G>A",
"hgvs_p": "p.Ala857Thr",
"transcript": "ENST00000686926.1",
"protein_id": "ENSP00000509122.1",
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},
{
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"protein_coding": true,
"strand": false,
"consequences": [
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],
"exon_rank": 3,
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"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIG4",
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"hgvs_c": "c.2569G>A",
"hgvs_p": "p.Ala857Thr",
"transcript": "ENST00000687164.1",
"protein_id": "ENSP00000508512.1",
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"aa_end": null,
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},
{
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"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
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"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIG4",
"gene_hgnc_id": 6601,
"hgvs_c": "c.2569G>A",
"hgvs_p": "p.Ala857Thr",
"transcript": "ENST00000687822.1",
"protein_id": "ENSP00000509344.1",
"transcript_support_level": null,
"aa_start": 857,
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"aa_length": 911,
"cds_start": 2569,
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"cdna_start": 4561,
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"cdna_length": 5799,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIG4",
"gene_hgnc_id": 6601,
"hgvs_c": "c.2569G>A",
"hgvs_p": "p.Ala857Thr",
"transcript": "ENST00000688396.1",
"protein_id": "ENSP00000509564.1",
"transcript_support_level": null,
"aa_start": 857,
"aa_end": null,
"aa_length": 911,
"cds_start": 2569,
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"cdna_start": 3178,
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"cdna_length": 4416,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
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],
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"computational_score_selected": 0.0017314553260803223,
"computational_prediction_selected": "Benign",
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"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.126,
"revel_prediction": "Benign",
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"bayesdelnoaf_score": -0.52,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.656,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
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"acmg_score": -20,
"acmg_classification": "Benign",
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"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
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"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000442234.6",
"gene_symbol": "LIG4",
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"effects": [
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],
"inheritance_mode": "AR",
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}
],
"clinvar_disease": "DNA ligase IV deficiency,Severe combined immunodeficiency due to DCLRE1C deficiency,not provided",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:6",
"phenotype_combined": "Severe combined immunodeficiency due to DCLRE1C deficiency|DNA ligase IV deficiency|not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}