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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: 5-137883389-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=137883389&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 137883389,
"ref": "T",
"alt": "C",
"effect": "synonymous_variant",
"transcript": "ENST00000239926.9",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MYOT",
"gene_hgnc_id": 12399,
"hgvs_c": "c.822T>C",
"hgvs_p": "p.Ser274Ser",
"transcript": "NM_006790.3",
"protein_id": "NP_006781.1",
"transcript_support_level": null,
"aa_start": 274,
"aa_end": null,
"aa_length": 498,
"cds_start": 822,
"cds_end": null,
"cds_length": 1497,
"cdna_start": 1127,
"cdna_end": null,
"cdna_length": 2268,
"mane_select": "ENST00000239926.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MYOT",
"gene_hgnc_id": 12399,
"hgvs_c": "c.822T>C",
"hgvs_p": "p.Ser274Ser",
"transcript": "ENST00000239926.9",
"protein_id": "ENSP00000239926.4",
"transcript_support_level": 1,
"aa_start": 274,
"aa_end": null,
"aa_length": 498,
"cds_start": 822,
"cds_end": null,
"cds_length": 1497,
"cdna_start": 1127,
"cdna_end": null,
"cdna_length": 2268,
"mane_select": "NM_006790.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MYOT",
"gene_hgnc_id": 12399,
"hgvs_c": "c.477T>C",
"hgvs_p": "p.Ser159Ser",
"transcript": "NM_001300911.2",
"protein_id": "NP_001287840.1",
"transcript_support_level": null,
"aa_start": 159,
"aa_end": null,
"aa_length": 383,
"cds_start": 477,
"cds_end": null,
"cds_length": 1152,
"cdna_start": 776,
"cdna_end": null,
"cdna_length": 1917,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MYOT",
"gene_hgnc_id": 12399,
"hgvs_c": "c.477T>C",
"hgvs_p": "p.Ser159Ser",
"transcript": "ENST00000515645.1",
"protein_id": "ENSP00000426281.1",
"transcript_support_level": 2,
"aa_start": 159,
"aa_end": null,
"aa_length": 383,
"cds_start": 477,
"cds_end": null,
"cds_length": 1152,
"cdna_start": 760,
"cdna_end": null,
"cdna_length": 1578,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MYOT",
"gene_hgnc_id": 12399,
"hgvs_c": "c.270T>C",
"hgvs_p": "p.Ser90Ser",
"transcript": "NM_001135940.2",
"protein_id": "NP_001129412.1",
"transcript_support_level": null,
"aa_start": 90,
"aa_end": null,
"aa_length": 314,
"cds_start": 270,
"cds_end": null,
"cds_length": 945,
"cdna_start": 645,
"cdna_end": null,
"cdna_length": 1786,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MYOT",
"gene_hgnc_id": 12399,
"hgvs_c": "c.270T>C",
"hgvs_p": "p.Ser90Ser",
"transcript": "ENST00000421631.6",
"protein_id": "ENSP00000391185.2",
"transcript_support_level": 2,
"aa_start": 90,
"aa_end": null,
"aa_length": 314,
"cds_start": 270,
"cds_end": null,
"cds_length": 945,
"cdna_start": 647,
"cdna_end": null,
"cdna_length": 1474,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MYOT",
"gene_hgnc_id": 12399,
"hgvs_c": "c.237T>C",
"hgvs_p": "p.Ser79Ser",
"transcript": "XM_017010061.2",
"protein_id": "XP_016865550.1",
"transcript_support_level": null,
"aa_start": 79,
"aa_end": null,
"aa_length": 303,
"cds_start": 237,
"cds_end": null,
"cds_length": 912,
"cdna_start": 376,
"cdna_end": null,
"cdna_length": 1517,
"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": "MYOT",
"gene_hgnc_id": 12399,
"hgvs_c": "n.387T>C",
"hgvs_p": null,
"transcript": "ENST00000503748.1",
"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": 582,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"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": "PKD2L2-DT",
"gene_hgnc_id": 55557,
"hgvs_c": "n.610A>G",
"hgvs_p": null,
"transcript": "ENST00000508281.3",
"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": 4275,
"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": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MYOT",
"gene_hgnc_id": 12399,
"hgvs_c": "n.257T>C",
"hgvs_p": null,
"transcript": "ENST00000511254.1",
"protein_id": null,
"transcript_support_level": 3,
"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": 579,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD2L2-DT",
"gene_hgnc_id": 55557,
"hgvs_c": "n.656A>G",
"hgvs_p": null,
"transcript": "ENST00000728450.1",
"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": 1252,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"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": "PKD2L2-DT",
"gene_hgnc_id": 55557,
"hgvs_c": "n.529A>G",
"hgvs_p": null,
"transcript": "ENST00000728451.1",
"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": 1123,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD2L2-DT",
"gene_hgnc_id": 55557,
"hgvs_c": "n.535A>G",
"hgvs_p": null,
"transcript": "XR_007058950.1",
"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": 8495,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "MYOT",
"gene_hgnc_id": 12399,
"hgvs_c": "n.506+2524T>C",
"hgvs_p": null,
"transcript": "ENST00000509812.5",
"protein_id": null,
"transcript_support_level": 3,
"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": 563,
"mane_select": null,
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"biotype": null,
"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": 2,
"intron_rank_end": null,
"gene_symbol": "PKD2L2-DT",
"gene_hgnc_id": 55557,
"hgvs_c": "n.370+4771A>G",
"hgvs_p": null,
"transcript": "ENST00000514616.7",
"protein_id": null,
"transcript_support_level": 5,
"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": 2851,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PKD2L2-DT",
"gene_hgnc_id": 55557,
"hgvs_c": "n.317+4771A>G",
"hgvs_p": null,
"transcript": "ENST00000728404.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
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"aa_length": null,
"cds_start": -4,
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"cdna_start": null,
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"cdna_length": 1128,
"mane_select": null,
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"biotype": null,
"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": 6,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PKD2L2-DT",
"gene_hgnc_id": 55557,
"hgvs_c": "n.301+4771A>G",
"hgvs_p": null,
"transcript": "ENST00000728405.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
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"aa_length": null,
"cds_start": -4,
"cds_end": null,
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"cdna_start": null,
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"cdna_length": 1953,
"mane_select": null,
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"biotype": null,
"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": 6,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PKD2L2-DT",
"gene_hgnc_id": 55557,
"hgvs_c": "n.308+4771A>G",
"hgvs_p": null,
"transcript": "ENST00000728406.1",
"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": 1228,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": 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": 2,
"intron_rank_end": null,
"gene_symbol": "PKD2L2-DT",
"gene_hgnc_id": 55557,
"hgvs_c": "n.361+4771A>G",
"hgvs_p": null,
"transcript": "ENST00000728407.1",
"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": 6,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PKD2L2-DT",
"gene_hgnc_id": 55557,
"hgvs_c": "n.302+4771A>G",
"hgvs_p": null,
"transcript": "ENST00000728408.1",
"protein_id": null,
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"aa_length": null,
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"mane_select": null,
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"biotype": null,
"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": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PKD2L2-DT",
"gene_hgnc_id": 55557,
"hgvs_c": "n.188+5758A>G",
"hgvs_p": null,
"transcript": "ENST00000728409.1",
"protein_id": null,
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"biotype": null,
"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": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PKD2L2-DT",
"gene_hgnc_id": 55557,
"hgvs_c": "n.186+5758A>G",
"hgvs_p": null,
"transcript": "ENST00000728410.1",
"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": 625,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PKD2L2-DT",
"gene_hgnc_id": 55557,
"hgvs_c": "n.356+4771A>G",
"hgvs_p": null,
"transcript": "ENST00000728411.1",
"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": 781,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
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"aa_alt": null,
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],
"gene_symbol": "MYOT",
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"dbsnp": "rs138678049",
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"computational_score_selected": -0.5400000214576721,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
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"alphamissense_score": null,
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"bayesdelnoaf_score": -0.54,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.759,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
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"dbscsnv_ada_prediction": null,
"apogee2_score": null,
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"mitotip_score": null,
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"acmg_score": -21,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BS1,BS2",
"acmg_by_gene": [
{
"score": -21,
"benign_score": 21,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000239926.9",
"gene_symbol": "MYOT",
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"effects": [
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],
"inheritance_mode": "AD",
"hgvs_c": "c.822T>C",
"hgvs_p": "p.Ser274Ser"
},
{
"score": -16,
"benign_score": 16,
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"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000508281.3",
"gene_symbol": "PKD2L2-DT",
"hgnc_id": 55557,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.610A>G",
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}
],
"clinvar_disease": "Myofibrillar myopathy 3,not provided,not specified",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:1 B:5",
"phenotype_combined": "not specified|not provided|Myofibrillar myopathy 3",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}