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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: 5-139283108-T-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=139283108&ref=T&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 139283108,
"ref": "T",
"alt": "G",
"effect": "intron_variant",
"transcript": "ENST00000502929.5",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SNHG4",
"gene_hgnc_id": 32964,
"hgvs_c": "n.592T>G",
"hgvs_p": null,
"transcript": "ENST00000505522.6",
"protein_id": null,
"transcript_support_level": 1,
"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": 2383,
"mane_select": null,
"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": 20,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "MATR3",
"gene_hgnc_id": 6912,
"hgvs_c": "c.-404+3979T>G",
"hgvs_p": null,
"transcript": "ENST00000502929.5",
"protein_id": "ENSP00000422319.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 895,
"cds_start": -4,
"cds_end": null,
"cds_length": 2688,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4373,
"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": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SNHG4",
"gene_hgnc_id": 32964,
"hgvs_c": "n.729T>G",
"hgvs_p": null,
"transcript": "ENST00000507197.5",
"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": 865,
"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": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SNHG4",
"gene_hgnc_id": 32964,
"hgvs_c": "n.622T>G",
"hgvs_p": null,
"transcript": "NR_036536.2",
"protein_id": null,
"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": 2414,
"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": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SNHG4",
"gene_hgnc_id": 32964,
"hgvs_c": "n.746T>G",
"hgvs_p": null,
"transcript": "NR_182751.1",
"protein_id": null,
"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": 2538,
"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": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SNHG4",
"gene_hgnc_id": 32964,
"hgvs_c": "n.812T>G",
"hgvs_p": null,
"transcript": "NR_182752.1",
"protein_id": null,
"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": 2604,
"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": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SNHG4",
"gene_hgnc_id": 32964,
"hgvs_c": "n.461T>G",
"hgvs_p": null,
"transcript": "NR_182753.1",
"protein_id": null,
"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": 2253,
"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": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SNHG4",
"gene_hgnc_id": 32964,
"hgvs_c": "n.1199T>G",
"hgvs_p": null,
"transcript": "NR_182754.1",
"protein_id": null,
"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": 2991,
"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": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SNHG4",
"gene_hgnc_id": 32964,
"hgvs_c": "n.922T>G",
"hgvs_p": null,
"transcript": "NR_182755.1",
"protein_id": null,
"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": 2714,
"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": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SNHG4",
"gene_hgnc_id": 32964,
"hgvs_c": "n.873T>G",
"hgvs_p": null,
"transcript": "NR_182756.1",
"protein_id": null,
"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": 2665,
"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": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SNHG4",
"gene_hgnc_id": 32964,
"hgvs_c": "n.997T>G",
"hgvs_p": null,
"transcript": "NR_182757.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
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"cdna_start": null,
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"cdna_length": 2789,
"mane_select": null,
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"biotype": null,
"feature": null
},
{
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"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "MATR3",
"gene_hgnc_id": 6912,
"hgvs_c": "c.-178+6958T>G",
"hgvs_p": null,
"transcript": "NM_001400441.1",
"protein_id": "NP_001387370.1",
"transcript_support_level": null,
"aa_start": null,
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"cds_start": -4,
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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": 18,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "MATR3",
"gene_hgnc_id": 6912,
"hgvs_c": "c.-178+3979T>G",
"hgvs_p": null,
"transcript": "NM_001400442.1",
"protein_id": "NP_001387371.1",
"transcript_support_level": null,
"aa_start": null,
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"aa_length": 895,
"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": [
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],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "MATR3",
"gene_hgnc_id": 6912,
"hgvs_c": "c.-178+6958T>G",
"hgvs_p": null,
"transcript": "NM_001400443.1",
"protein_id": "NP_001387372.1",
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"cds_start": -4,
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},
{
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"strand": true,
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],
"exon_rank": null,
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"intron_rank": 4,
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"gene_symbol": "MATR3",
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"hgvs_c": "c.-301+3979T>G",
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"transcript": "NM_001400444.1",
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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": 19,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "MATR3",
"gene_hgnc_id": 6912,
"hgvs_c": "c.-301+3979T>G",
"hgvs_p": null,
"transcript": "ENST00000394800.6",
"protein_id": "ENSP00000378279.2",
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},
{
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],
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"intron_rank": 3,
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"gene_symbol": "MATR3",
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"hgvs_c": "c.-178+3979T>G",
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"transcript": "NM_001194954.2",
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},
{
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"protein_coding": true,
"strand": true,
"consequences": [
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],
"exon_rank": null,
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"exon_count": 17,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "MATR3",
"gene_hgnc_id": 6912,
"hgvs_c": "c.-301+6958T>G",
"hgvs_p": null,
"transcript": "NM_001400447.1",
"protein_id": "NP_001387376.1",
"transcript_support_level": null,
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},
{
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"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "MATR3",
"gene_hgnc_id": 6912,
"hgvs_c": "c.-301+3979T>G",
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"transcript": "NM_001400448.1",
"protein_id": "NP_001387377.1",
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},
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"consequences": [
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],
"exon_rank": null,
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"intron_rank": 4,
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"gene_symbol": "MATR3",
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},
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"strand": true,
"consequences": [
"intron_variant"
],
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"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "MATR3",
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},
{
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"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
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"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "MATR3",
"gene_hgnc_id": 6912,
"hgvs_c": "c.-301+3050T>G",
"hgvs_p": null,
"transcript": "NM_001400452.1",
"protein_id": "NP_001387381.1",
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"aa_start": null,
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"cds_start": -4,
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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": 16,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "MATR3",
"gene_hgnc_id": 6912,
"hgvs_c": "c.-178+6958T>G",
"hgvs_p": null,
"transcript": "NM_001400453.1",
"protein_id": "NP_001387382.1",
"transcript_support_level": null,
"aa_start": null,
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},
{
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},
{
"aa_ref": null,
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],
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"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
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"splice_prediction_selected": "Benign",
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"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.89,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.498,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
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"dbscsnv_ada_prediction": null,
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"acmg_score": -12,
"acmg_classification": "Benign",
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"acmg_by_gene": [
{
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"criteria": [
"BP4_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000502929.5",
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"effects": [
"intron_variant"
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"inheritance_mode": "AD",
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{
"score": -12,
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"criteria": [
"BP4_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000505522.6",
"gene_symbol": "SNHG4",
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"effects": [
"non_coding_transcript_exon_variant"
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"inheritance_mode": "",
"hgvs_c": "n.592T>G",
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{
"score": -12,
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"BP4_Strong",
"BA1"
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"verdict": "Benign",
"transcript": "ENST00000508744.1",
"gene_symbol": "SIL1",
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"intron_variant"
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"inheritance_mode": "AR",
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{
"score": -12,
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"criteria": [
"BP4_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "XR_007058956.1",
"gene_symbol": "LOC124901081",
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"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.347+2140A>C",
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}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}