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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: 3-9434401-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=9434401&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 9434401,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000402198.7",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD5",
"gene_hgnc_id": 25566,
"hgvs_c": "c.245C>T",
"hgvs_p": "p.Pro82Leu",
"transcript": "NM_001080517.3",
"protein_id": "NP_001073986.1",
"transcript_support_level": null,
"aa_start": 82,
"aa_end": null,
"aa_length": 1442,
"cds_start": 245,
"cds_end": null,
"cds_length": 4329,
"cdna_start": 784,
"cdna_end": null,
"cdna_length": 6931,
"mane_select": "ENST00000402198.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD5",
"gene_hgnc_id": 25566,
"hgvs_c": "c.245C>T",
"hgvs_p": "p.Pro82Leu",
"transcript": "ENST00000402198.7",
"protein_id": "ENSP00000385852.2",
"transcript_support_level": 5,
"aa_start": 82,
"aa_end": null,
"aa_length": 1442,
"cds_start": 245,
"cds_end": null,
"cds_length": 4329,
"cdna_start": 784,
"cdna_end": null,
"cdna_length": 6931,
"mane_select": "NM_001080517.3",
"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": 1,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD5",
"gene_hgnc_id": 25566,
"hgvs_c": "n.409C>T",
"hgvs_p": null,
"transcript": "ENST00000493918.5",
"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": 4861,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_premature_start_codon_gain_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD5",
"gene_hgnc_id": 25566,
"hgvs_c": "c.-89C>T",
"hgvs_p": null,
"transcript": "NM_001292043.2",
"protein_id": "NP_001278972.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1344,
"cds_start": -4,
"cds_end": null,
"cds_length": 4035,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 7187,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_premature_start_codon_gain_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD5",
"gene_hgnc_id": 25566,
"hgvs_c": "c.-130C>T",
"hgvs_p": null,
"transcript": "NM_001349451.2",
"protein_id": "NP_001336380.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1344,
"cds_start": -4,
"cds_end": null,
"cds_length": 4035,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 7228,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_premature_start_codon_gain_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD5",
"gene_hgnc_id": 25566,
"hgvs_c": "c.-130C>T",
"hgvs_p": null,
"transcript": "XM_047448499.1",
"protein_id": "XP_047304455.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1363,
"cds_start": -4,
"cds_end": null,
"cds_length": 4092,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6313,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_premature_start_codon_gain_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD5",
"gene_hgnc_id": 25566,
"hgvs_c": "c.-130C>T",
"hgvs_p": null,
"transcript": "XM_011533933.2",
"protein_id": "XP_011532235.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1350,
"cds_start": -4,
"cds_end": null,
"cds_length": 4053,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6274,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD5",
"gene_hgnc_id": 25566,
"hgvs_c": "c.302C>T",
"hgvs_p": "p.Pro101Leu",
"transcript": "NM_001437635.1",
"protein_id": "NP_001424564.1",
"transcript_support_level": null,
"aa_start": 101,
"aa_end": null,
"aa_length": 1480,
"cds_start": 302,
"cds_end": null,
"cds_length": 4443,
"cdna_start": 841,
"cdna_end": null,
"cdna_length": 7037,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD5",
"gene_hgnc_id": 25566,
"hgvs_c": "c.302C>T",
"hgvs_p": "p.Pro101Leu",
"transcript": "NM_001437633.1",
"protein_id": "NP_001424562.1",
"transcript_support_level": null,
"aa_start": 101,
"aa_end": null,
"aa_length": 1474,
"cds_start": 302,
"cds_end": null,
"cds_length": 4425,
"cdna_start": 841,
"cdna_end": null,
"cdna_length": 7019,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD5",
"gene_hgnc_id": 25566,
"hgvs_c": "c.302C>T",
"hgvs_p": "p.Pro101Leu",
"transcript": "ENST00000682536.1",
"protein_id": "ENSP00000507956.1",
"transcript_support_level": null,
"aa_start": 101,
"aa_end": null,
"aa_length": 1474,
"cds_start": 302,
"cds_end": null,
"cds_length": 4425,
"cdna_start": 575,
"cdna_end": null,
"cdna_length": 5624,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD5",
"gene_hgnc_id": 25566,
"hgvs_c": "c.245C>T",
"hgvs_p": "p.Pro82Leu",
"transcript": "NM_001437643.1",
"protein_id": "NP_001424572.1",
"transcript_support_level": null,
"aa_start": 82,
"aa_end": null,
"aa_length": 1461,
"cds_start": 245,
"cds_end": null,
"cds_length": 4386,
"cdna_start": 1319,
"cdna_end": null,
"cdna_length": 7515,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD5",
"gene_hgnc_id": 25566,
"hgvs_c": "c.302C>T",
"hgvs_p": "p.Pro101Leu",
"transcript": "ENST00000407969.5",
"protein_id": "ENSP00000384114.1",
"transcript_support_level": 5,
"aa_start": 101,
"aa_end": null,
"aa_length": 1461,
"cds_start": 302,
"cds_end": null,
"cds_length": 4386,
"cdna_start": 316,
"cdna_end": null,
"cdna_length": 6463,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD5",
"gene_hgnc_id": 25566,
"hgvs_c": "c.245C>T",
"hgvs_p": "p.Pro82Leu",
"transcript": "NM_001437701.1",
"protein_id": "NP_001424630.1",
"transcript_support_level": null,
"aa_start": 82,
"aa_end": null,
"aa_length": 1455,
"cds_start": 245,
"cds_end": null,
"cds_length": 4368,
"cdna_start": 784,
"cdna_end": null,
"cdna_length": 6962,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD5",
"gene_hgnc_id": 25566,
"hgvs_c": "c.245C>T",
"hgvs_p": "p.Pro82Leu",
"transcript": "ENST00000406341.5",
"protein_id": "ENSP00000383939.1",
"transcript_support_level": 5,
"aa_start": 82,
"aa_end": null,
"aa_length": 1442,
"cds_start": 245,
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"cds_length": 4329,
"cdna_start": 435,
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"cdna_length": 6582,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD5",
"gene_hgnc_id": 25566,
"hgvs_c": "c.245C>T",
"hgvs_p": "p.Pro82Leu",
"transcript": "ENST00000684055.1",
"protein_id": "ENSP00000507953.1",
"transcript_support_level": null,
"aa_start": 82,
"aa_end": null,
"aa_length": 931,
"cds_start": 245,
"cds_end": null,
"cds_length": 2796,
"cdna_start": 361,
"cdna_end": null,
"cdna_length": 4416,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD5",
"gene_hgnc_id": 25566,
"hgvs_c": "c.323C>T",
"hgvs_p": "p.Pro108Leu",
"transcript": "XM_047448466.1",
"protein_id": "XP_047304422.1",
"transcript_support_level": null,
"aa_start": 108,
"aa_end": null,
"aa_length": 1500,
"cds_start": 323,
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"cdna_start": 5394,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD5",
"gene_hgnc_id": 25566,
"hgvs_c": "c.323C>T",
"hgvs_p": "p.Pro108Leu",
"transcript": "XM_047448467.1",
"protein_id": "XP_047304423.1",
"transcript_support_level": null,
"aa_start": 108,
"aa_end": null,
"aa_length": 1500,
"cds_start": 323,
"cds_end": null,
"cds_length": 4503,
"cdna_start": 4366,
"cdna_end": null,
"cdna_length": 10609,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD5",
"gene_hgnc_id": 25566,
"hgvs_c": "c.323C>T",
"hgvs_p": "p.Pro108Leu",
"transcript": "XM_047448468.1",
"protein_id": "XP_047304424.1",
"transcript_support_level": null,
"aa_start": 108,
"aa_end": null,
"aa_length": 1500,
"cds_start": 323,
"cds_end": null,
"cds_length": 4503,
"cdna_start": 6334,
"cdna_end": null,
"cdna_length": 12577,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD5",
"gene_hgnc_id": 25566,
"hgvs_c": "c.323C>T",
"hgvs_p": "p.Pro108Leu",
"transcript": "XM_047448469.1",
"protein_id": "XP_047304425.1",
"transcript_support_level": null,
"aa_start": 108,
"aa_end": null,
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"cds_start": 323,
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"cdna_start": 2257,
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"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD5",
"gene_hgnc_id": 25566,
"hgvs_c": "c.323C>T",
"hgvs_p": "p.Pro108Leu",
"transcript": "XM_047448470.1",
"protein_id": "XP_047304426.1",
"transcript_support_level": null,
"aa_start": 108,
"aa_end": null,
"aa_length": 1500,
"cds_start": 323,
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"cdna_start": 3919,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD5",
"gene_hgnc_id": 25566,
"hgvs_c": "c.323C>T",
"hgvs_p": "p.Pro108Leu",
"transcript": "XM_047448471.1",
"protein_id": "XP_047304427.1",
"transcript_support_level": null,
"aa_start": 108,
"aa_end": null,
"aa_length": 1500,
"cds_start": 323,
"cds_end": null,
"cds_length": 4503,
"cdna_start": 4618,
"cdna_end": null,
"cdna_length": 10861,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD5",
"gene_hgnc_id": 25566,
"hgvs_c": "c.323C>T",
"hgvs_p": "p.Pro108Leu",
"transcript": "XM_047448472.1",
"protein_id": "XP_047304428.1",
"transcript_support_level": null,
"aa_start": 108,
"aa_end": null,
"aa_length": 1500,
"cds_start": 323,
"cds_end": null,
"cds_length": 4503,
"cdna_start": 2032,
"cdna_end": null,
"cdna_length": 8275,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD5",
"gene_hgnc_id": 25566,
"hgvs_c": "c.302C>T",
"hgvs_p": "p.Pro101Leu",
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},
{
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}
],
"gene_symbol": "SETD5",
"gene_hgnc_id": 25566,
"dbsnp": "rs746405582",
"frequency_reference_population": 0.0000061967853,
"hom_count_reference_population": 0,
"allele_count_reference_population": 10,
"gnomad_exomes_af": 0.00000547309,
"gnomad_genomes_af": 0.0000131543,
"gnomad_exomes_ac": 8,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.15797469019889832,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.26,
"revel_prediction": "Benign",
"alphamissense_score": 0.1706,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.21,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 5.145,
"phylop100way_prediction": "Uncertain_significance",
"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": -6,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate,BS2",
"acmg_by_gene": [
{
"score": -6,
"benign_score": 6,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "ENST00000402198.7",
"gene_symbol": "SETD5",
"hgnc_id": 25566,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.245C>T",
"hgvs_p": "p.Pro82Leu"
}
],
"clinvar_disease": "not provided,not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:2",
"phenotype_combined": "not specified|not provided",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}