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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: 7-5982986-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=7&pos=5982986&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "7",
"pos": 5982986,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000265849.12",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMS2",
"gene_hgnc_id": 9122,
"hgvs_c": "c.2012C>T",
"hgvs_p": "p.Thr671Met",
"transcript": "NM_000535.7",
"protein_id": "NP_000526.2",
"transcript_support_level": null,
"aa_start": 671,
"aa_end": null,
"aa_length": 862,
"cds_start": 2012,
"cds_end": null,
"cds_length": 2589,
"cdna_start": 2042,
"cdna_end": null,
"cdna_length": 5093,
"mane_select": "ENST00000265849.12",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMS2",
"gene_hgnc_id": 9122,
"hgvs_c": "c.2012C>T",
"hgvs_p": "p.Thr671Met",
"transcript": "ENST00000265849.12",
"protein_id": "ENSP00000265849.7",
"transcript_support_level": 1,
"aa_start": 671,
"aa_end": null,
"aa_length": 862,
"cds_start": 2012,
"cds_end": null,
"cds_length": 2589,
"cdna_start": 2042,
"cdna_end": null,
"cdna_length": 5093,
"mane_select": "NM_000535.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMS2",
"gene_hgnc_id": 9122,
"hgvs_c": "c.809C>T",
"hgvs_p": "p.Thr270Met",
"transcript": "ENST00000382321.5",
"protein_id": "ENSP00000371758.4",
"transcript_support_level": 1,
"aa_start": 270,
"aa_end": null,
"aa_length": 461,
"cds_start": 809,
"cds_end": null,
"cds_length": 1386,
"cdna_start": 809,
"cdna_end": null,
"cdna_length": 1386,
"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": 13,
"intron_rank": 11,
"intron_rank_end": null,
"gene_symbol": "PMS2",
"gene_hgnc_id": 9122,
"hgvs_c": "n.1678+4101C>T",
"hgvs_p": null,
"transcript": "ENST00000406569.8",
"protein_id": "ENSP00000514464.1",
"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": 2101,
"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": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PMS2",
"gene_hgnc_id": 9122,
"hgvs_c": "n.63-81C>T",
"hgvs_p": null,
"transcript": "ENST00000469652.1",
"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": 93,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMS2",
"gene_hgnc_id": 9122,
"hgvs_c": "c.2198C>T",
"hgvs_p": "p.Thr733Met",
"transcript": "NM_001406866.1",
"protein_id": "NP_001393795.1",
"transcript_support_level": null,
"aa_start": 733,
"aa_end": null,
"aa_length": 924,
"cds_start": 2198,
"cds_end": null,
"cds_length": 2775,
"cdna_start": 2228,
"cdna_end": null,
"cdna_length": 5279,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMS2",
"gene_hgnc_id": 9122,
"hgvs_c": "c.2198C>T",
"hgvs_p": "p.Thr733Met",
"transcript": "ENST00000699839.1",
"protein_id": "ENSP00000514637.1",
"transcript_support_level": null,
"aa_start": 733,
"aa_end": null,
"aa_length": 924,
"cds_start": 2198,
"cds_end": null,
"cds_length": 2775,
"cdna_start": 2263,
"cdna_end": null,
"cdna_length": 3597,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMS2",
"gene_hgnc_id": 9122,
"hgvs_c": "c.2012C>T",
"hgvs_p": "p.Thr671Met",
"transcript": "NM_001322014.2",
"protein_id": "NP_001308943.1",
"transcript_support_level": null,
"aa_start": 671,
"aa_end": null,
"aa_length": 873,
"cds_start": 2012,
"cds_end": null,
"cds_length": 2622,
"cdna_start": 2042,
"cdna_end": null,
"cdna_length": 5126,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMS2",
"gene_hgnc_id": 9122,
"hgvs_c": "c.2012C>T",
"hgvs_p": "p.Thr671Met",
"transcript": "ENST00000699766.1",
"protein_id": "ENSP00000514574.1",
"transcript_support_level": null,
"aa_start": 671,
"aa_end": null,
"aa_length": 873,
"cds_start": 2012,
"cds_end": null,
"cds_length": 2622,
"cdna_start": 2115,
"cdna_end": null,
"cdna_length": 5167,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMS2",
"gene_hgnc_id": 9122,
"hgvs_c": "c.2036C>T",
"hgvs_p": "p.Thr679Met",
"transcript": "NM_001406868.1",
"protein_id": "NP_001393797.1",
"transcript_support_level": null,
"aa_start": 679,
"aa_end": null,
"aa_length": 870,
"cds_start": 2036,
"cds_end": null,
"cds_length": 2613,
"cdna_start": 2066,
"cdna_end": null,
"cdna_length": 5117,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMS2",
"gene_hgnc_id": 9122,
"hgvs_c": "c.2009C>T",
"hgvs_p": "p.Thr670Met",
"transcript": "ENST00000699840.2",
"protein_id": "ENSP00000514638.2",
"transcript_support_level": null,
"aa_start": 670,
"aa_end": null,
"aa_length": 861,
"cds_start": 2009,
"cds_end": null,
"cds_length": 2586,
"cdna_start": 2077,
"cdna_end": null,
"cdna_length": 2812,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMS2",
"gene_hgnc_id": 9122,
"hgvs_c": "c.1904C>T",
"hgvs_p": "p.Thr635Met",
"transcript": "NM_001406869.1",
"protein_id": "NP_001393798.1",
"transcript_support_level": null,
"aa_start": 635,
"aa_end": null,
"aa_length": 826,
"cds_start": 1904,
"cds_end": null,
"cds_length": 2481,
"cdna_start": 1934,
"cdna_end": null,
"cdna_length": 4985,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMS2",
"gene_hgnc_id": 9122,
"hgvs_c": "c.1904C>T",
"hgvs_p": "p.Thr635Met",
"transcript": "ENST00000699930.2",
"protein_id": "ENSP00000514695.2",
"transcript_support_level": null,
"aa_start": 635,
"aa_end": null,
"aa_length": 826,
"cds_start": 1904,
"cds_end": null,
"cds_length": 2481,
"cdna_start": 1984,
"cdna_end": null,
"cdna_length": 5035,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMS2",
"gene_hgnc_id": 9122,
"hgvs_c": "c.1856C>T",
"hgvs_p": "p.Thr619Met",
"transcript": "NM_001406870.1",
"protein_id": "NP_001393799.1",
"transcript_support_level": null,
"aa_start": 619,
"aa_end": null,
"aa_length": 821,
"cds_start": 1856,
"cds_end": null,
"cds_length": 2466,
"cdna_start": 1886,
"cdna_end": null,
"cdna_length": 4970,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMS2",
"gene_hgnc_id": 9122,
"hgvs_c": "c.2012C>T",
"hgvs_p": "p.Thr671Met",
"transcript": "NM_001406871.1",
"protein_id": "NP_001393800.1",
"transcript_support_level": null,
"aa_start": 671,
"aa_end": null,
"aa_length": 814,
"cds_start": 2012,
"cds_end": null,
"cds_length": 2445,
"cdna_start": 2042,
"cdna_end": null,
"cdna_length": 4949,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMS2",
"gene_hgnc_id": 9122,
"hgvs_c": "c.2012C>T",
"hgvs_p": "p.Thr671Met",
"transcript": "ENST00000699768.1",
"protein_id": "ENSP00000514576.1",
"transcript_support_level": null,
"aa_start": 671,
"aa_end": null,
"aa_length": 814,
"cds_start": 2012,
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"cdna_start": 2115,
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"cdna_length": 4990,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMS2",
"gene_hgnc_id": 9122,
"hgvs_c": "c.1856C>T",
"hgvs_p": "p.Thr619Met",
"transcript": "NM_001322006.2",
"protein_id": "NP_001308935.1",
"transcript_support_level": null,
"aa_start": 619,
"aa_end": null,
"aa_length": 810,
"cds_start": 1856,
"cds_end": null,
"cds_length": 2433,
"cdna_start": 1886,
"cdna_end": null,
"cdna_length": 4937,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMS2",
"gene_hgnc_id": 9122,
"hgvs_c": "c.1856C>T",
"hgvs_p": "p.Thr619Met",
"transcript": "ENST00000699752.1",
"protein_id": "ENSP00000514561.1",
"transcript_support_level": null,
"aa_start": 619,
"aa_end": null,
"aa_length": 810,
"cds_start": 1856,
"cds_end": null,
"cds_length": 2433,
"cdna_start": 1886,
"cdna_end": null,
"cdna_length": 4907,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMS2",
"gene_hgnc_id": 9122,
"hgvs_c": "c.1844C>T",
"hgvs_p": "p.Thr615Met",
"transcript": "NM_001406874.1",
"protein_id": "NP_001393803.1",
"transcript_support_level": null,
"aa_start": 615,
"aa_end": null,
"aa_length": 806,
"cds_start": 1844,
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"cdna_start": 1874,
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"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMS2",
"gene_hgnc_id": 9122,
"hgvs_c": "c.1844C>T",
"hgvs_p": "p.Thr615Met",
"transcript": "ENST00000699827.1",
"protein_id": "ENSP00000514628.1",
"transcript_support_level": null,
"aa_start": 615,
"aa_end": null,
"aa_length": 806,
"cds_start": 1844,
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"cdna_start": 1924,
"cdna_end": null,
"cdna_length": 2659,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMS2",
"gene_hgnc_id": 9122,
"hgvs_c": "c.1814C>T",
"hgvs_p": "p.Thr605Met",
"transcript": "NM_001406873.1",
"protein_id": "NP_001393802.1",
"transcript_support_level": null,
"aa_start": 605,
"aa_end": null,
"aa_length": 796,
"cds_start": 1814,
"cds_end": null,
"cds_length": 2391,
"cdna_start": 1844,
"cdna_end": null,
"cdna_length": 4895,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMS2",
"gene_hgnc_id": 9122,
"hgvs_c": "c.1814C>T",
"hgvs_p": "p.Thr605Met",
"transcript": "ENST00000699754.1",
"protein_id": "ENSP00000514563.1",
"transcript_support_level": null,
"aa_start": 605,
"aa_end": null,
"aa_length": 796,
"cds_start": 1814,
"cds_end": null,
"cds_length": 2391,
"cdna_start": 1859,
"cdna_end": null,
"cdna_length": 4880,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMS2",
"gene_hgnc_id": 9122,
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],
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"hom_count_reference_population": 1,
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"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
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"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
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"revel_prediction": "Benign",
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"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.15,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 5.698,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.1,
"spliceai_max_prediction": "Benign",
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"mitotip_score": null,
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"acmg_classification": "Likely_benign",
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"acmg_by_gene": [
{
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"pathogenic_score": 0,
"criteria": [
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"verdict": "Likely_benign",
"transcript": "ENST00000265849.12",
"gene_symbol": "PMS2",
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"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:20 LB:4 B:2 O:1",
"phenotype_combined": "Hereditary cancer-predisposing syndrome|Lynch syndrome 1|Hereditary nonpolyposis colorectal neoplasms|not specified|Mismatch repair cancer syndrome 1;Lynch syndrome 4|Lynch syndrome 4|not provided|Cancer or benign tumor|Lynch syndrome;Mismatch repair cancer syndrome 4|Breast and/or ovarian cancer|Hereditary breast ovarian cancer syndrome",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}