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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: 12-112418839-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=112418839&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 4,
"criteria": [
"BP4_Strong"
],
"effects": [
"5_prime_UTR_variant"
],
"gene_symbol": "RPL6",
"hgnc_id": 10362,
"hgvs_c": "c.-1368C>G",
"hgvs_p": null,
"inheritance_mode": "AD",
"pathogenic_score": 0,
"score": -4,
"transcript": "ENST00000955984.1",
"verdict": "Likely_benign"
},
{
"benign_score": 4,
"criteria": [
"BP4_Strong"
],
"effects": [
"non_coding_transcript_exon_variant"
],
"gene_symbol": "PTPN11",
"hgnc_id": 9644,
"hgvs_c": "n.331G>C",
"hgvs_p": null,
"inheritance_mode": "AD",
"pathogenic_score": 0,
"score": -4,
"transcript": "ENST00000531326.1",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Strong",
"acmg_score": -4,
"allele_count_reference_population": 7,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "C",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.68,
"chr": "12",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.6800000071525574,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": null,
"aa_end": null,
"aa_length": 288,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2273,
"cdna_start": null,
"cds_end": null,
"cds_length": 867,
"cds_start": null,
"consequences": [
"5_prime_UTR_variant"
],
"exon_count": 9,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000955984.1",
"gene_hgnc_id": 10362,
"gene_symbol": "RPL6",
"hgvs_c": "c.-1368C>G",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000626043.1",
"strand": false,
"transcript": "ENST00000955984.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 573,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000531326.1",
"gene_hgnc_id": 9644,
"gene_symbol": "PTPN11",
"hgvs_c": "n.331G>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000531326.1",
"transcript_support_level": 4
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 593,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6073,
"cdna_start": null,
"cds_end": null,
"cds_length": 1782,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 16,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_002834.5",
"gene_hgnc_id": 9644,
"gene_symbol": "PTPN11",
"hgvs_c": "c.-273G>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000351677.7",
"protein_coding": true,
"protein_id": "NP_002825.3",
"strand": true,
"transcript": "NM_002834.5",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 593,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 6073,
"cdna_start": null,
"cds_end": null,
"cds_length": 1782,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 16,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000351677.7",
"gene_hgnc_id": 9644,
"gene_symbol": "PTPN11",
"hgvs_c": "c.-273G>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_002834.5",
"protein_coding": true,
"protein_id": "ENSP00000340944.3",
"strand": true,
"transcript": "ENST00000351677.7",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 460,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1876,
"cdna_start": null,
"cds_end": null,
"cds_length": 1383,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 11,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000392597.5",
"gene_hgnc_id": 9644,
"gene_symbol": "PTPN11",
"hgvs_c": "c.-273G>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000376376.1",
"strand": true,
"transcript": "ENST00000392597.5",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 671,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6274,
"cdna_start": null,
"cds_end": null,
"cds_length": 2016,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 17,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000690210.1",
"gene_hgnc_id": 9644,
"gene_symbol": "PTPN11",
"hgvs_c": "c.-273G>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000509272.1",
"strand": true,
"transcript": "ENST00000690210.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 597,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6085,
"cdna_start": null,
"cds_end": null,
"cds_length": 1794,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 16,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_001330437.2",
"gene_hgnc_id": 9644,
"gene_symbol": "PTPN11",
"hgvs_c": "c.-273G>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001317366.1",
"strand": true,
"transcript": "NM_001330437.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 596,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6120,
"cdna_start": null,
"cds_end": null,
"cds_length": 1791,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 16,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000882517.1",
"gene_hgnc_id": 9644,
"gene_symbol": "PTPN11",
"hgvs_c": "c.-273G>C",
"hgvs_p": null,
"intron_rank": null,
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"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000552576.1",
"strand": true,
"transcript": "ENST00000882517.1",
"transcript_support_level": null
},
{
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"aa_ref": null,
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"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6070,
"cdna_start": null,
"cds_end": null,
"cds_length": 1779,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 16,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_001374625.1",
"gene_hgnc_id": 9644,
"gene_symbol": "PTPN11",
"hgvs_c": "c.-273G>C",
"hgvs_p": null,
"intron_rank": null,
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"mane_plus": null,
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"protein_coding": true,
"protein_id": "NP_001361554.1",
"strand": true,
"transcript": "NM_001374625.1",
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},
{
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"cdna_length": 6129,
"cdna_start": null,
"cds_end": null,
"cds_length": 1779,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 16,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000882515.1",
"gene_hgnc_id": 9644,
"gene_symbol": "PTPN11",
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"mane_plus": null,
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"protein_coding": true,
"protein_id": "ENSP00000552574.1",
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"transcript": "ENST00000882515.1",
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},
{
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"cdna_start": null,
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"consequences": [
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],
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"feature": "ENST00000639857.2",
"gene_hgnc_id": 9644,
"gene_symbol": "PTPN11",
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"mane_plus": null,
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},
{
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"consequences": [
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],
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"feature": "ENST00000882516.1",
"gene_hgnc_id": 9644,
"gene_symbol": "PTPN11",
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},
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],
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"feature": "ENST00000914890.1",
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"mane_plus": null,
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"protein_coding": true,
"protein_id": "ENSP00000584949.1",
"strand": true,
"transcript": "ENST00000914890.1",
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},
{
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],
"exon_count": 15,
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"feature": "ENST00000687906.1",
"gene_hgnc_id": 9644,
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},
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"consequences": [
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],
"exon_count": 15,
"exon_rank": null,
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"feature": "ENST00000971611.1",
"gene_hgnc_id": 9644,
"gene_symbol": "PTPN11",
"hgvs_c": "c.-273G>C",
"hgvs_p": null,
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"mane_plus": null,
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"protein_coding": true,
"protein_id": "ENSP00000641670.1",
"strand": true,
"transcript": "ENST00000971611.1",
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},
{
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"consequences": [
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],
"exon_count": 15,
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"feature": "ENST00000882518.1",
"gene_hgnc_id": 9644,
"gene_symbol": "PTPN11",
"hgvs_c": "c.-273G>C",
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"mane_plus": null,
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"protein_coding": true,
"protein_id": "ENSP00000552577.1",
"strand": true,
"transcript": "ENST00000882518.1",
"transcript_support_level": null
},
{
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"consequences": [
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],
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"feature": "ENST00000971614.1",
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},
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],
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"feature": "ENST00000688597.1",
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"strand": true,
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},
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"consequences": [
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],
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"feature": "ENST00000914889.1",
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"protein_coding": true,
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"strand": true,
"transcript": "ENST00000914889.1",
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},
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"cds_end": null,
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"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 11,
"exon_rank": null,
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"feature": "NM_080601.3",
"gene_hgnc_id": 9644,
"gene_symbol": "PTPN11",
"hgvs_c": "c.-273G>C",
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"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_542168.1",
"strand": true,
"transcript": "NM_080601.3",
"transcript_support_level": null
},
{
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"biotype": "protein_coding",
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"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 12,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000971615.1",
"gene_hgnc_id": 9644,
"gene_symbol": "PTPN11",
"hgvs_c": "c.-273G>C",
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