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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: 2-231000439-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=231000439&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 231000439,
"ref": "T",
"alt": "C",
"effect": "synonymous_variant",
"transcript": "NM_139073.5",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPATA3",
"gene_hgnc_id": 17884,
"hgvs_c": "c.375T>C",
"hgvs_p": "p.Arg125Arg",
"transcript": "NM_139073.5",
"protein_id": "NP_620712.2",
"transcript_support_level": null,
"aa_start": 125,
"aa_end": null,
"aa_length": 192,
"cds_start": 375,
"cds_end": null,
"cds_length": 579,
"cdna_start": 488,
"cdna_end": null,
"cdna_length": 1629,
"mane_select": "ENST00000433428.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPATA3",
"gene_hgnc_id": 17884,
"hgvs_c": "c.375T>C",
"hgvs_p": "p.Arg125Arg",
"transcript": "ENST00000433428.7",
"protein_id": "ENSP00000403804.2",
"transcript_support_level": 1,
"aa_start": 125,
"aa_end": null,
"aa_length": 192,
"cds_start": 375,
"cds_end": null,
"cds_length": 579,
"cdna_start": 488,
"cdna_end": null,
"cdna_length": 1629,
"mane_select": "NM_139073.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPATA3",
"gene_hgnc_id": 17884,
"hgvs_c": "c.375T>C",
"hgvs_p": "p.Arg125Arg",
"transcript": "ENST00000424440.5",
"protein_id": "ENSP00000399514.1",
"transcript_support_level": 1,
"aa_start": 125,
"aa_end": null,
"aa_length": 192,
"cds_start": 375,
"cds_end": null,
"cds_length": 579,
"cdna_start": 488,
"cdna_end": null,
"cdna_length": 1011,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPATA3",
"gene_hgnc_id": 17884,
"hgvs_c": "c.864T>C",
"hgvs_p": "p.Arg288Arg",
"transcript": "ENST00000645363.1",
"protein_id": "ENSP00000494655.1",
"transcript_support_level": null,
"aa_start": 288,
"aa_end": null,
"aa_length": 355,
"cds_start": 864,
"cds_end": null,
"cds_length": 1068,
"cdna_start": 864,
"cdna_end": null,
"cdna_length": 1068,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPATA3",
"gene_hgnc_id": 17884,
"hgvs_c": "c.375T>C",
"hgvs_p": "p.Arg125Arg",
"transcript": "ENST00000452881.5",
"protein_id": "ENSP00000388895.1",
"transcript_support_level": 2,
"aa_start": 125,
"aa_end": null,
"aa_length": 192,
"cds_start": 375,
"cds_end": null,
"cds_length": 579,
"cdna_start": 483,
"cdna_end": null,
"cdna_length": 1618,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPATA3",
"gene_hgnc_id": 17884,
"hgvs_c": "c.375T>C",
"hgvs_p": "p.Arg125Arg",
"transcript": "ENST00000455816.1",
"protein_id": "ENSP00000388741.1",
"transcript_support_level": 5,
"aa_start": 125,
"aa_end": null,
"aa_length": 192,
"cds_start": 375,
"cds_end": null,
"cds_length": 579,
"cdna_start": 375,
"cdna_end": null,
"cdna_length": 766,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPATA3",
"gene_hgnc_id": 17884,
"hgvs_c": "c.375T>C",
"hgvs_p": "p.Arg125Arg",
"transcript": "XM_047443397.1",
"protein_id": "XP_047299353.1",
"transcript_support_level": null,
"aa_start": 125,
"aa_end": null,
"aa_length": 213,
"cds_start": 375,
"cds_end": null,
"cds_length": 642,
"cdna_start": 488,
"cdna_end": null,
"cdna_length": 1602,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPATA3",
"gene_hgnc_id": 17884,
"hgvs_c": "c.375T>C",
"hgvs_p": "p.Arg125Arg",
"transcript": "XM_047443398.1",
"protein_id": "XP_047299354.1",
"transcript_support_level": null,
"aa_start": 125,
"aa_end": null,
"aa_length": 213,
"cds_start": 375,
"cds_end": null,
"cds_length": 642,
"cdna_start": 488,
"cdna_end": null,
"cdna_length": 1002,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPATA3",
"gene_hgnc_id": 17884,
"hgvs_c": "c.375T>C",
"hgvs_p": "p.Arg125Arg",
"transcript": "XM_005246303.3",
"protein_id": "XP_005246360.1",
"transcript_support_level": null,
"aa_start": 125,
"aa_end": null,
"aa_length": 192,
"cds_start": 375,
"cds_end": null,
"cds_length": 579,
"cdna_start": 488,
"cdna_end": null,
"cdna_length": 1549,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPATA3",
"gene_hgnc_id": 17884,
"hgvs_c": "c.375T>C",
"hgvs_p": "p.Arg125Arg",
"transcript": "XM_017003363.3",
"protein_id": "XP_016858852.1",
"transcript_support_level": null,
"aa_start": 125,
"aa_end": null,
"aa_length": 192,
"cds_start": 375,
"cds_end": null,
"cds_length": 579,
"cdna_start": 488,
"cdna_end": null,
"cdna_length": 944,
"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": "SPATA3",
"gene_hgnc_id": 17884,
"hgvs_c": "n.97T>C",
"hgvs_p": null,
"transcript": "ENST00000454918.1",
"protein_id": "ENSP00000395644.1",
"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": 332,
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPATA3",
"gene_hgnc_id": 17884,
"hgvs_c": "n.488T>C",
"hgvs_p": null,
"transcript": "XR_001738624.3",
"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": 1024,
"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": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPATA3",
"gene_hgnc_id": 17884,
"hgvs_c": "n.488T>C",
"hgvs_p": null,
"transcript": "XR_001738627.3",
"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": 1497,
"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": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPATA3",
"gene_hgnc_id": 17884,
"hgvs_c": "n.488T>C",
"hgvs_p": null,
"transcript": "XR_001738628.2",
"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,
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"cdna_length": 1319,
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPATA3",
"gene_hgnc_id": 17884,
"hgvs_c": "n.488T>C",
"hgvs_p": null,
"transcript": "XR_002959241.2",
"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": 1211,
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPATA3",
"gene_hgnc_id": 17884,
"hgvs_c": "n.488T>C",
"hgvs_p": null,
"transcript": "XR_007069639.1",
"protein_id": null,
"transcript_support_level": null,
"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": 1682,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPATA3",
"gene_hgnc_id": 17884,
"hgvs_c": "n.488T>C",
"hgvs_p": null,
"transcript": "XR_007069640.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
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"cdna_start": null,
"cdna_end": null,
"cdna_length": 1081,
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPATA3",
"gene_hgnc_id": 17884,
"hgvs_c": "n.488T>C",
"hgvs_p": null,
"transcript": "XR_007069641.1",
"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": 1025,
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPATA3",
"gene_hgnc_id": 17884,
"hgvs_c": "n.488T>C",
"hgvs_p": null,
"transcript": "XR_007069642.1",
"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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"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": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPATA3",
"gene_hgnc_id": 17884,
"hgvs_c": "n.488T>C",
"hgvs_p": null,
"transcript": "XR_922856.3",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
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"cdna_start": null,
"cdna_end": null,
"cdna_length": 1791,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SPATA3",
"gene_hgnc_id": 17884,
"hgvs_c": "c.200-2245T>C",
"hgvs_p": null,
"transcript": "ENST00000440792.5",
"protein_id": "ENSP00000404510.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 104,
"cds_start": -4,
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"cdna_start": null,
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"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SPATA3",
"gene_hgnc_id": 17884,
"hgvs_c": "c.146-2245T>C",
"hgvs_p": null,
"transcript": "ENST00000423134.1",
"protein_id": "ENSP00000411374.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 86,
"cds_start": -4,
"cds_end": null,
"cds_length": 261,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 433,
"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": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SPATA3",
"gene_hgnc_id": 17884,
"hgvs_c": "n.242+629T>C",
"hgvs_p": null,
"transcript": "ENST00000409956.1",
"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": 436,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SPATA3",
"gene_hgnc_id": 17884,
"dbsnp": "rs201768791",
"frequency_reference_population": 0.00028660064,
"hom_count_reference_population": 1,
"allele_count_reference_population": 444,
"gnomad_exomes_af": 0.000282035,
"gnomad_genomes_af": 0.000328502,
"gnomad_exomes_ac": 394,
"gnomad_genomes_ac": 50,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 1,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.6200000047683716,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.62,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.137,
"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": -7,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Moderate,BP7",
"acmg_by_gene": [
{
"score": -7,
"benign_score": 7,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Moderate",
"BP7"
],
"verdict": "Benign",
"transcript": "NM_139073.5",
"gene_symbol": "SPATA3",
"hgnc_id": 17884,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.375T>C",
"hgvs_p": "p.Arg125Arg"
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}