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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: 2-85888869-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=85888869&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 85888869,
"ref": "G",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000638572.2",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ST3GAL5",
"gene_hgnc_id": 10872,
"hgvs_c": "c.37C>A",
"hgvs_p": "p.Pro13Thr",
"transcript": "NM_003896.4",
"protein_id": "NP_003887.3",
"transcript_support_level": null,
"aa_start": 13,
"aa_end": null,
"aa_length": 418,
"cds_start": 37,
"cds_end": null,
"cds_length": 1257,
"cdna_start": 122,
"cdna_end": null,
"cdna_length": 4366,
"mane_select": "ENST00000638572.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ST3GAL5",
"gene_hgnc_id": 10872,
"hgvs_c": "c.37C>A",
"hgvs_p": "p.Pro13Thr",
"transcript": "ENST00000638572.2",
"protein_id": "ENSP00000491316.1",
"transcript_support_level": 1,
"aa_start": 13,
"aa_end": null,
"aa_length": 418,
"cds_start": 37,
"cds_end": null,
"cds_length": 1257,
"cdna_start": 122,
"cdna_end": null,
"cdna_length": 4366,
"mane_select": "NM_003896.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ST3GAL5",
"gene_hgnc_id": 10872,
"hgvs_c": "c.34C>A",
"hgvs_p": "p.Pro12Thr",
"transcript": "ENST00000639305.1",
"protein_id": "ENSP00000492244.1",
"transcript_support_level": 5,
"aa_start": 12,
"aa_end": null,
"aa_length": 406,
"cds_start": 34,
"cds_end": null,
"cds_length": 1221,
"cdna_start": 35,
"cdna_end": null,
"cdna_length": 2160,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ST3GAL5",
"gene_hgnc_id": 10872,
"hgvs_c": "c.37C>A",
"hgvs_p": "p.Pro13Thr",
"transcript": "ENST00000377332.8",
"protein_id": "ENSP00000366549.4",
"transcript_support_level": 5,
"aa_start": 13,
"aa_end": null,
"aa_length": 378,
"cds_start": 37,
"cds_end": null,
"cds_length": 1137,
"cdna_start": 90,
"cdna_end": null,
"cdna_length": 2165,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ST3GAL5",
"gene_hgnc_id": 10872,
"hgvs_c": "c.37C>A",
"hgvs_p": "p.Pro13Thr",
"transcript": "NM_001363847.1",
"protein_id": "NP_001350776.1",
"transcript_support_level": null,
"aa_start": 13,
"aa_end": null,
"aa_length": 365,
"cds_start": 37,
"cds_end": null,
"cds_length": 1098,
"cdna_start": 166,
"cdna_end": null,
"cdna_length": 2238,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ST3GAL5",
"gene_hgnc_id": 10872,
"hgvs_c": "c.37C>A",
"hgvs_p": "p.Pro13Thr",
"transcript": "ENST00000639119.1",
"protein_id": "ENSP00000492045.1",
"transcript_support_level": 5,
"aa_start": 13,
"aa_end": null,
"aa_length": 365,
"cds_start": 37,
"cds_end": null,
"cds_length": 1098,
"cdna_start": 95,
"cdna_end": null,
"cdna_length": 2131,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ST3GAL5",
"gene_hgnc_id": 10872,
"hgvs_c": "c.13C>A",
"hgvs_p": "p.Pro5Thr",
"transcript": "ENST00000640315.1",
"protein_id": "ENSP00000492089.1",
"transcript_support_level": 5,
"aa_start": 5,
"aa_end": null,
"aa_length": 223,
"cds_start": 13,
"cds_end": null,
"cds_length": 672,
"cdna_start": 13,
"cdna_end": null,
"cdna_length": 1890,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ST3GAL5",
"gene_hgnc_id": 10872,
"hgvs_c": "c.37C>A",
"hgvs_p": "p.Pro13Thr",
"transcript": "XM_047446241.1",
"protein_id": "XP_047302197.1",
"transcript_support_level": null,
"aa_start": 13,
"aa_end": null,
"aa_length": 252,
"cds_start": 37,
"cds_end": null,
"cds_length": 759,
"cdna_start": 166,
"cdna_end": null,
"cdna_length": 972,
"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": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ST3GAL5",
"gene_hgnc_id": 10872,
"hgvs_c": "n.37C>A",
"hgvs_p": null,
"transcript": "ENST00000306262.10",
"protein_id": "ENSP00000306247.6",
"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": 779,
"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": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ST3GAL5",
"gene_hgnc_id": 10872,
"hgvs_c": "n.37C>A",
"hgvs_p": null,
"transcript": "ENST00000433665.6",
"protein_id": "ENSP00000408635.1",
"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": 544,
"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": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ST3GAL5",
"gene_hgnc_id": 10872,
"hgvs_c": "n.42C>A",
"hgvs_p": null,
"transcript": "ENST00000461892.6",
"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": 871,
"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": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ST3GAL5",
"gene_hgnc_id": 10872,
"hgvs_c": "n.37C>A",
"hgvs_p": null,
"transcript": "ENST00000473122.6",
"protein_id": "ENSP00000491314.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
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"cds_length": null,
"cdna_start": null,
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"cdna_length": 1085,
"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": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ST3GAL5",
"gene_hgnc_id": 10872,
"hgvs_c": "n.48C>A",
"hgvs_p": null,
"transcript": "ENST00000484728.6",
"protein_id": null,
"transcript_support_level": 2,
"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": 588,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ST3GAL5",
"gene_hgnc_id": 10872,
"hgvs_c": "n.37C>A",
"hgvs_p": null,
"transcript": "ENST00000638227.1",
"protein_id": "ENSP00000492602.1",
"transcript_support_level": 5,
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},
{
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"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ST3GAL5",
"gene_hgnc_id": 10872,
"hgvs_c": "n.37C>A",
"hgvs_p": null,
"transcript": "ENST00000638484.1",
"protein_id": "ENSP00000492635.1",
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"aa_start": null,
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"cdna_start": 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": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
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"gene_symbol": "ST3GAL5",
"gene_hgnc_id": 10872,
"hgvs_c": "n.37C>A",
"hgvs_p": null,
"transcript": "ENST00000638542.1",
"protein_id": "ENSP00000492468.1",
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},
{
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"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
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"exon_count": 8,
"intron_rank": null,
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"gene_symbol": "ST3GAL5",
"gene_hgnc_id": 10872,
"hgvs_c": "n.34C>A",
"hgvs_p": null,
"transcript": "ENST00000638659.1",
"protein_id": "ENSP00000491395.1",
"transcript_support_level": 5,
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"mane_select": null,
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"feature": null
},
{
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"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ST3GAL5",
"gene_hgnc_id": 10872,
"hgvs_c": "n.34C>A",
"hgvs_p": null,
"transcript": "ENST00000638678.1",
"protein_id": "ENSP00000492847.1",
"transcript_support_level": 5,
"aa_start": null,
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"cds_start": -4,
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"mane_select": null,
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},
{
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"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ST3GAL5",
"gene_hgnc_id": 10872,
"hgvs_c": "n.37C>A",
"hgvs_p": null,
"transcript": "ENST00000638855.1",
"protein_id": "ENSP00000490979.1",
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},
{
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"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
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"exon_count": 8,
"intron_rank": null,
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"gene_symbol": "ST3GAL5",
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"hgvs_c": "n.37C>A",
"hgvs_p": null,
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"protein_id": "ENSP00000492209.1",
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},
{
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"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
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"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ST3GAL5",
"gene_hgnc_id": 10872,
"hgvs_c": "n.37C>A",
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"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ST3GAL5",
"gene_hgnc_id": 10872,
"hgvs_c": "n.37C>A",
"hgvs_p": null,
"transcript": "ENST00000639311.1",
"protein_id": "ENSP00000491398.1",
"transcript_support_level": 5,
"aa_start": null,
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"aa_length": null,
"cds_start": -4,
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"cdna_length": 2347,
"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": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ST3GAL5",
"gene_hgnc_id": 10872,
"hgvs_c": "n.37C>A",
"hgvs_p": null,
"transcript": "ENST00000639421.1",
"protein_id": "ENSP00000491029.1",
"transcript_support_level": 5,
"aa_start": null,
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{
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},
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},
{
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},
{
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],
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}
],
"gene_symbol": "ST3GAL5",
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"dbsnp": "rs559756386",
"frequency_reference_population": 0.000004115836,
"hom_count_reference_population": 0,
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"gnomad_exomes_ac": 5,
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"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.13401898741722107,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.051,
"revel_prediction": "Benign",
"alphamissense_score": 0.1099,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.57,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.114,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
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"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000638572.2",
"gene_symbol": "ST3GAL5",
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"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
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"hgvs_p": "p.Pro13Thr"
}
],
"clinvar_disease": "GM3 synthase deficiency",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "GM3 synthase deficiency",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}