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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: 19-5211608-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=5211608&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 5211608,
"ref": "C",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_002850.4",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 33,
"exon_rank_end": null,
"exon_count": 38,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRS",
"gene_hgnc_id": 9681,
"hgvs_c": "c.5216G>C",
"hgvs_p": "p.Ser1739Thr",
"transcript": "NM_002850.4",
"protein_id": "NP_002841.3",
"transcript_support_level": null,
"aa_start": 1739,
"aa_end": null,
"aa_length": 1948,
"cds_start": 5216,
"cds_end": null,
"cds_length": 5847,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000262963.11",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_002850.4"
},
{
"aa_ref": "S",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 33,
"exon_rank_end": null,
"exon_count": 38,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRS",
"gene_hgnc_id": 9681,
"hgvs_c": "c.5216G>C",
"hgvs_p": "p.Ser1739Thr",
"transcript": "ENST00000262963.11",
"protein_id": "ENSP00000262963.8",
"transcript_support_level": 5,
"aa_start": 1739,
"aa_end": null,
"aa_length": 1948,
"cds_start": 5216,
"cds_end": null,
"cds_length": 5847,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_002850.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000262963.11"
},
{
"aa_ref": "S",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 32,
"exon_rank_end": null,
"exon_count": 37,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRS",
"gene_hgnc_id": 9681,
"hgvs_c": "c.5216G>C",
"hgvs_p": "p.Ser1739Thr",
"transcript": "ENST00000587303.5",
"protein_id": "ENSP00000467537.1",
"transcript_support_level": 1,
"aa_start": 1739,
"aa_end": null,
"aa_length": 1948,
"cds_start": 5216,
"cds_end": null,
"cds_length": 5847,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000587303.5"
},
{
"aa_ref": "S",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRS",
"gene_hgnc_id": 9681,
"hgvs_c": "c.5102G>C",
"hgvs_p": "p.Ser1701Thr",
"transcript": "ENST00000588012.5",
"protein_id": "ENSP00000465443.1",
"transcript_support_level": 1,
"aa_start": 1701,
"aa_end": null,
"aa_length": 1910,
"cds_start": 5102,
"cds_end": null,
"cds_length": 5733,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000588012.5"
},
{
"aa_ref": "S",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRS",
"gene_hgnc_id": 9681,
"hgvs_c": "c.3875G>C",
"hgvs_p": "p.Ser1292Thr",
"transcript": "ENST00000592099.5",
"protein_id": "ENSP00000467398.1",
"transcript_support_level": 1,
"aa_start": 1292,
"aa_end": null,
"aa_length": 1501,
"cds_start": 3875,
"cds_end": null,
"cds_length": 4506,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000592099.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRS",
"gene_hgnc_id": 9681,
"hgvs_c": "n.4157G>C",
"hgvs_p": null,
"transcript": "ENST00000588552.5",
"protein_id": null,
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000588552.5"
},
{
"aa_ref": "S",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRS",
"gene_hgnc_id": 9681,
"hgvs_c": "c.5150G>C",
"hgvs_p": "p.Ser1717Thr",
"transcript": "NM_001394011.1",
"protein_id": "NP_001380940.1",
"transcript_support_level": null,
"aa_start": 1717,
"aa_end": null,
"aa_length": 1926,
"cds_start": 5150,
"cds_end": null,
"cds_length": 5781,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001394011.1"
},
{
"aa_ref": "S",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRS",
"gene_hgnc_id": 9681,
"hgvs_c": "c.5129G>C",
"hgvs_p": "p.Ser1710Thr",
"transcript": "NM_001394012.1",
"protein_id": "NP_001380941.1",
"transcript_support_level": null,
"aa_start": 1710,
"aa_end": null,
"aa_length": 1919,
"cds_start": 5129,
"cds_end": null,
"cds_length": 5760,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001394012.1"
},
{
"aa_ref": "S",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRS",
"gene_hgnc_id": 9681,
"hgvs_c": "c.5102G>C",
"hgvs_p": "p.Ser1701Thr",
"transcript": "NM_130854.3",
"protein_id": "NP_570924.2",
"transcript_support_level": null,
"aa_start": 1701,
"aa_end": null,
"aa_length": 1910,
"cds_start": 5102,
"cds_end": null,
"cds_length": 5733,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_130854.3"
},
{
"aa_ref": "S",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRS",
"gene_hgnc_id": 9681,
"hgvs_c": "c.5090G>C",
"hgvs_p": "p.Ser1697Thr",
"transcript": "NM_001394013.1",
"protein_id": "NP_001380942.1",
"transcript_support_level": null,
"aa_start": 1697,
"aa_end": null,
"aa_length": 1906,
"cds_start": 5090,
"cds_end": null,
"cds_length": 5721,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001394013.1"
},
{
"aa_ref": "S",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRS",
"gene_hgnc_id": 9681,
"hgvs_c": "c.5090G>C",
"hgvs_p": "p.Ser1697Thr",
"transcript": "ENST00000919618.1",
"protein_id": "ENSP00000589677.1",
"transcript_support_level": null,
"aa_start": 1697,
"aa_end": null,
"aa_length": 1906,
"cds_start": 5090,
"cds_end": null,
"cds_length": 5721,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000919618.1"
},
{
"aa_ref": "S",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRS",
"gene_hgnc_id": 9681,
"hgvs_c": "c.4388G>C",
"hgvs_p": "p.Ser1463Thr",
"transcript": "ENST00000850941.1",
"protein_id": "ENSP00000521026.1",
"transcript_support_level": null,
"aa_start": 1463,
"aa_end": null,
"aa_length": 1672,
"cds_start": 4388,
"cds_end": null,
"cds_length": 5019,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000850941.1"
},
{
"aa_ref": "S",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRS",
"gene_hgnc_id": 9681,
"hgvs_c": "c.3911G>C",
"hgvs_p": "p.Ser1304Thr",
"transcript": "ENST00000919619.1",
"protein_id": "ENSP00000589678.1",
"transcript_support_level": null,
"aa_start": 1304,
"aa_end": null,
"aa_length": 1513,
"cds_start": 3911,
"cds_end": null,
"cds_length": 4542,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000919619.1"
},
{
"aa_ref": "S",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRS",
"gene_hgnc_id": 9681,
"hgvs_c": "c.3887G>C",
"hgvs_p": "p.Ser1296Thr",
"transcript": "NM_130855.3",
"protein_id": "NP_570925.2",
"transcript_support_level": null,
"aa_start": 1296,
"aa_end": null,
"aa_length": 1505,
"cds_start": 3887,
"cds_end": null,
"cds_length": 4518,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_130855.3"
},
{
"aa_ref": "S",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRS",
"gene_hgnc_id": 9681,
"hgvs_c": "c.3875G>C",
"hgvs_p": "p.Ser1292Thr",
"transcript": "NM_130853.3",
"protein_id": "NP_570923.2",
"transcript_support_level": null,
"aa_start": 1292,
"aa_end": null,
"aa_length": 1501,
"cds_start": 3875,
"cds_end": null,
"cds_length": 4506,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_130853.3"
},
{
"aa_ref": "S",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 31,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRS",
"gene_hgnc_id": 9681,
"hgvs_c": "c.5189G>C",
"hgvs_p": "p.Ser1730Thr",
"transcript": "XM_017027065.2",
"protein_id": "XP_016882554.1",
"transcript_support_level": null,
"aa_start": 1730,
"aa_end": null,
"aa_length": 1939,
"cds_start": 5189,
"cds_end": null,
"cds_length": 5820,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017027065.2"
},
{
"aa_ref": "S",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 31,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRS",
"gene_hgnc_id": 9681,
"hgvs_c": "c.5189G>C",
"hgvs_p": "p.Ser1730Thr",
"transcript": "XM_017027066.2",
"protein_id": "XP_016882555.1",
"transcript_support_level": null,
"aa_start": 1730,
"aa_end": null,
"aa_length": 1939,
"cds_start": 5189,
"cds_end": null,
"cds_length": 5820,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017027066.2"
},
{
"aa_ref": "S",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 31,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRS",
"gene_hgnc_id": 9681,
"hgvs_c": "c.5189G>C",
"hgvs_p": "p.Ser1730Thr",
"transcript": "XM_017027067.2",
"protein_id": "XP_016882556.1",
"transcript_support_level": null,
"aa_start": 1730,
"aa_end": null,
"aa_length": 1939,
"cds_start": 5189,
"cds_end": null,
"cds_length": 5820,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017027067.2"
},
{
"aa_ref": "S",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 30,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRS",
"gene_hgnc_id": 9681,
"hgvs_c": "c.5177G>C",
"hgvs_p": "p.Ser1726Thr",
"transcript": "XM_005259600.3",
"protein_id": "XP_005259657.1",
"transcript_support_level": null,
"aa_start": 1726,
"aa_end": null,
"aa_length": 1935,
"cds_start": 5177,
"cds_end": null,
"cds_length": 5808,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005259600.3"
},
{
"aa_ref": "S",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 30,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRS",
"gene_hgnc_id": 9681,
"hgvs_c": "c.5177G>C",
"hgvs_p": "p.Ser1726Thr",
"transcript": "XM_017027068.2",
"protein_id": "XP_016882557.1",
"transcript_support_level": null,
"aa_start": 1726,
"aa_end": null,
"aa_length": 1935,
"cds_start": 5177,
"cds_end": null,
"cds_length": 5808,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017027068.2"
},
{
"aa_ref": "S",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 30,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRS",
"gene_hgnc_id": 9681,
"hgvs_c": "c.5177G>C",
"hgvs_p": "p.Ser1726Thr",
"transcript": "XM_047439155.1",
"protein_id": "XP_047295111.1",
"transcript_support_level": null,
"aa_start": 1726,
"aa_end": null,
"aa_length": 1935,
"cds_start": 5177,
"cds_end": null,
"cds_length": 5808,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047439155.1"
},
{
"aa_ref": "S",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 30,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRS",
"gene_hgnc_id": 9681,
"hgvs_c": "c.5177G>C",
"hgvs_p": "p.Ser1726Thr",
"transcript": "XM_047439156.1",
"protein_id": "XP_047295112.1",
"transcript_support_level": null,
"aa_start": 1726,
"aa_end": null,
"aa_length": 1935,
"cds_start": 5177,
"cds_end": null,
"cds_length": 5808,
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"computational_score_selected": 0.9064698815345764,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.363,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.3701,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.29,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 7.809,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 4,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3_Moderate",
"acmg_by_gene": [
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_002850.4",
"gene_symbol": "PTPRS",
"hgnc_id": 9681,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.5216G>C",
"hgvs_p": "p.Ser1739Thr"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}