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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: 3-49417595-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=49417595&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 49417595,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000273588.9",
"consequences": [
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AMT",
"gene_hgnc_id": 473,
"hgvs_c": "c.1157T>C",
"hgvs_p": "p.Met386Thr",
"transcript": "NM_000481.4",
"protein_id": "NP_000472.2",
"transcript_support_level": null,
"aa_start": 386,
"aa_end": null,
"aa_length": 403,
"cds_start": 1157,
"cds_end": null,
"cds_length": 1212,
"cdna_start": 1180,
"cdna_end": null,
"cdna_length": 1997,
"mane_select": "ENST00000273588.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AMT",
"gene_hgnc_id": 473,
"hgvs_c": "c.1157T>C",
"hgvs_p": "p.Met386Thr",
"transcript": "ENST00000273588.9",
"protein_id": "ENSP00000273588.3",
"transcript_support_level": 1,
"aa_start": 386,
"aa_end": null,
"aa_length": 403,
"cds_start": 1157,
"cds_end": null,
"cds_length": 1212,
"cdna_start": 1180,
"cdna_end": null,
"cdna_length": 1997,
"mane_select": "NM_000481.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000283189",
"gene_hgnc_id": null,
"hgvs_c": "c.1394T>C",
"hgvs_p": "p.Met465Thr",
"transcript": "ENST00000636166.1",
"protein_id": "ENSP00000490106.1",
"transcript_support_level": 5,
"aa_start": 465,
"aa_end": null,
"aa_length": 482,
"cds_start": 1394,
"cds_end": null,
"cds_length": 1449,
"cdna_start": 1465,
"cdna_end": null,
"cdna_length": 2266,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "AMT",
"gene_hgnc_id": 473,
"hgvs_c": "c.1137+20T>C",
"hgvs_p": null,
"transcript": "ENST00000395338.7",
"protein_id": "ENSP00000378747.2",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 386,
"cds_start": -4,
"cds_end": null,
"cds_length": 1161,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1831,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AMT",
"gene_hgnc_id": 473,
"hgvs_c": "c.1076T>C",
"hgvs_p": "p.Met359Thr",
"transcript": "ENST00000638063.1",
"protein_id": "ENSP00000489760.1",
"transcript_support_level": 5,
"aa_start": 359,
"aa_end": null,
"aa_length": 376,
"cds_start": 1076,
"cds_end": null,
"cds_length": 1131,
"cdna_start": 1086,
"cdna_end": null,
"cdna_length": 1783,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AMT",
"gene_hgnc_id": 473,
"hgvs_c": "c.1025T>C",
"hgvs_p": "p.Met342Thr",
"transcript": "NM_001164710.2",
"protein_id": "NP_001158182.1",
"transcript_support_level": null,
"aa_start": 342,
"aa_end": null,
"aa_length": 359,
"cds_start": 1025,
"cds_end": null,
"cds_length": 1080,
"cdna_start": 1048,
"cdna_end": null,
"cdna_length": 1865,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AMT",
"gene_hgnc_id": 473,
"hgvs_c": "c.1025T>C",
"hgvs_p": "p.Met342Thr",
"transcript": "ENST00000458307.6",
"protein_id": "ENSP00000415619.2",
"transcript_support_level": 2,
"aa_start": 342,
"aa_end": null,
"aa_length": 359,
"cds_start": 1025,
"cds_end": null,
"cds_length": 1080,
"cdna_start": 1044,
"cdna_end": null,
"cdna_length": 1860,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AMT",
"gene_hgnc_id": 473,
"hgvs_c": "c.1013T>C",
"hgvs_p": "p.Met338Thr",
"transcript": "ENST00000538581.6",
"protein_id": "ENSP00000443200.2",
"transcript_support_level": 2,
"aa_start": 338,
"aa_end": null,
"aa_length": 355,
"cds_start": 1013,
"cds_end": null,
"cds_length": 1068,
"cdna_start": 1222,
"cdna_end": null,
"cdna_length": 2038,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AMT",
"gene_hgnc_id": 473,
"hgvs_c": "c.1001T>C",
"hgvs_p": "p.Met334Thr",
"transcript": "ENST00000636865.1",
"protein_id": "ENSP00000490601.1",
"transcript_support_level": 5,
"aa_start": 334,
"aa_end": null,
"aa_length": 351,
"cds_start": 1001,
"cds_end": null,
"cds_length": 1056,
"cdna_start": 1148,
"cdna_end": null,
"cdna_length": 1914,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AMT",
"gene_hgnc_id": 473,
"hgvs_c": "c.1001T>C",
"hgvs_p": "p.Met334Thr",
"transcript": "ENST00000637682.1",
"protein_id": "ENSP00000489856.1",
"transcript_support_level": 5,
"aa_start": 334,
"aa_end": null,
"aa_length": 351,
"cds_start": 1001,
"cds_end": null,
"cds_length": 1056,
"cdna_start": 1008,
"cdna_end": null,
"cdna_length": 1823,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AMT",
"gene_hgnc_id": 473,
"hgvs_c": "c.989T>C",
"hgvs_p": "p.Met330Thr",
"transcript": "NM_001164711.2",
"protein_id": "NP_001158183.1",
"transcript_support_level": null,
"aa_start": 330,
"aa_end": null,
"aa_length": 347,
"cds_start": 989,
"cds_end": null,
"cds_length": 1044,
"cdna_start": 1012,
"cdna_end": null,
"cdna_length": 1829,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AMT",
"gene_hgnc_id": 473,
"hgvs_c": "c.989T>C",
"hgvs_p": "p.Met330Thr",
"transcript": "ENST00000636522.1",
"protein_id": "ENSP00000489758.1",
"transcript_support_level": 2,
"aa_start": 330,
"aa_end": null,
"aa_length": 347,
"cds_start": 989,
"cds_end": null,
"cds_length": 1044,
"cdna_start": 1012,
"cdna_end": null,
"cdna_length": 1620,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AMT",
"gene_hgnc_id": 473,
"hgvs_c": "c.719T>C",
"hgvs_p": "p.Met240Thr",
"transcript": "ENST00000636199.1",
"protein_id": "ENSP00000490871.1",
"transcript_support_level": 5,
"aa_start": 240,
"aa_end": null,
"aa_length": 257,
"cds_start": 719,
"cds_end": null,
"cds_length": 774,
"cdna_start": 729,
"cdna_end": null,
"cdna_length": 1546,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AMT",
"gene_hgnc_id": 473,
"hgvs_c": "c.674T>C",
"hgvs_p": "p.Met225Thr",
"transcript": "ENST00000636597.1",
"protein_id": "ENSP00000490251.1",
"transcript_support_level": 5,
"aa_start": 225,
"aa_end": null,
"aa_length": 242,
"cds_start": 674,
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"cdna_start": 715,
"cdna_end": null,
"cdna_length": 1509,
"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": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AMT",
"gene_hgnc_id": 473,
"hgvs_c": "n.*529T>C",
"hgvs_p": null,
"transcript": "ENST00000399379.7",
"protein_id": "ENSP00000399943.2",
"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": 977,
"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": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AMT",
"gene_hgnc_id": 473,
"hgvs_c": "n.3159T>C",
"hgvs_p": null,
"transcript": "ENST00000465925.6",
"protein_id": null,
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
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"cdna_start": null,
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"mane_select": null,
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"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": "AMT",
"gene_hgnc_id": 473,
"hgvs_c": "n.3773T>C",
"hgvs_p": null,
"transcript": "ENST00000473163.2",
"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,
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"cdna_length": 4544,
"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": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AMT",
"gene_hgnc_id": 473,
"hgvs_c": "n.1386T>C",
"hgvs_p": null,
"transcript": "ENST00000476127.6",
"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": 2152,
"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": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AMT",
"gene_hgnc_id": 473,
"hgvs_c": "n.1578T>C",
"hgvs_p": null,
"transcript": "ENST00000476226.6",
"protein_id": null,
"transcript_support_level": 5,
"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": 2379,
"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AMT",
"gene_hgnc_id": 473,
"hgvs_c": "n.2873T>C",
"hgvs_p": null,
"transcript": "ENST00000493046.6",
"protein_id": null,
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
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"cdna_start": null,
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"cdna_length": 3504,
"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": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AMT",
"gene_hgnc_id": 473,
"hgvs_c": "n.778T>C",
"hgvs_p": null,
"transcript": "ENST00000495436.5",
"protein_id": null,
"transcript_support_level": 2,
"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": 843,
"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": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AMT",
"gene_hgnc_id": 473,
"hgvs_c": "n.1995T>C",
"hgvs_p": null,
"transcript": "ENST00000635772.1",
"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": 2768,
"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": "AMT",
"gene_hgnc_id": 473,
"hgvs_c": "n.515T>C",
"hgvs_p": null,
"transcript": "ENST00000635798.1",
"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": 1276,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
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"computational_score_selected": 0.030603766441345215,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.133,
"revel_prediction": "Benign",
"alphamissense_score": 0.0969,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.39,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.752,
"phylop100way_prediction": "Benign",
"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": "Likely_benign",
"acmg_criteria": "BP4_Strong",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "ENST00000273588.9",
"gene_symbol": "AMT",
"hgnc_id": 473,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,Unknown",
"hgvs_c": "c.1157T>C",
"hgvs_p": "p.Met386Thr"
},
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "ENST00000636166.1",
"gene_symbol": "ENSG00000283189",
"hgnc_id": null,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.1394T>C",
"hgvs_p": "p.Met465Thr"
}
],
"clinvar_disease": "Glycine encephalopathy",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Glycine encephalopathy",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}