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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: 5-13917235-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=13917235&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 13917235,
"ref": "G",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "ENST00000265104.5",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 79,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAH5",
"gene_hgnc_id": 2950,
"hgvs_c": "c.997C>A",
"hgvs_p": "p.Arg333Arg",
"transcript": "NM_001369.3",
"protein_id": "NP_001360.1",
"transcript_support_level": null,
"aa_start": 333,
"aa_end": null,
"aa_length": 4624,
"cds_start": 997,
"cds_end": null,
"cds_length": 13875,
"cdna_start": 1247,
"cdna_end": null,
"cdna_length": 15781,
"mane_select": "ENST00000265104.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 79,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAH5",
"gene_hgnc_id": 2950,
"hgvs_c": "c.997C>A",
"hgvs_p": "p.Arg333Arg",
"transcript": "ENST00000265104.5",
"protein_id": "ENSP00000265104.4",
"transcript_support_level": 1,
"aa_start": 333,
"aa_end": null,
"aa_length": 4624,
"cds_start": 997,
"cds_end": null,
"cds_length": 13875,
"cdna_start": 1247,
"cdna_end": null,
"cdna_length": 15781,
"mane_select": "NM_001369.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 79,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAH5",
"gene_hgnc_id": 2950,
"hgvs_c": "c.952C>A",
"hgvs_p": "p.Arg318Arg",
"transcript": "ENST00000681290.1",
"protein_id": "ENSP00000505288.1",
"transcript_support_level": null,
"aa_start": 318,
"aa_end": null,
"aa_length": 4609,
"cds_start": 952,
"cds_end": null,
"cds_length": 13830,
"cdna_start": 1111,
"cdna_end": null,
"cdna_length": 15645,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 79,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAH5",
"gene_hgnc_id": 2950,
"hgvs_c": "c.1105C>A",
"hgvs_p": "p.Arg369Arg",
"transcript": "XM_005248262.4",
"protein_id": "XP_005248319.2",
"transcript_support_level": null,
"aa_start": 369,
"aa_end": null,
"aa_length": 4660,
"cds_start": 1105,
"cds_end": null,
"cds_length": 13983,
"cdna_start": 1111,
"cdna_end": null,
"cdna_length": 15645,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 79,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAH5",
"gene_hgnc_id": 2950,
"hgvs_c": "c.757C>A",
"hgvs_p": "p.Arg253Arg",
"transcript": "XM_047416886.1",
"protein_id": "XP_047272842.1",
"transcript_support_level": null,
"aa_start": 253,
"aa_end": null,
"aa_length": 4544,
"cds_start": 757,
"cds_end": null,
"cds_length": 13635,
"cdna_start": 1876,
"cdna_end": null,
"cdna_length": 16410,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 77,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAH5",
"gene_hgnc_id": 2950,
"hgvs_c": "c.1105C>A",
"hgvs_p": "p.Arg369Arg",
"transcript": "XM_017009177.2",
"protein_id": "XP_016864666.1",
"transcript_support_level": null,
"aa_start": 369,
"aa_end": null,
"aa_length": 4520,
"cds_start": 1105,
"cds_end": null,
"cds_length": 13563,
"cdna_start": 1111,
"cdna_end": null,
"cdna_length": 15225,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 73,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAH5",
"gene_hgnc_id": 2950,
"hgvs_c": "c.10C>A",
"hgvs_p": "p.Arg4Arg",
"transcript": "XM_017009179.3",
"protein_id": "XP_016864668.1",
"transcript_support_level": null,
"aa_start": 4,
"aa_end": null,
"aa_length": 4295,
"cds_start": 10,
"cds_end": null,
"cds_length": 12888,
"cdna_start": 219,
"cdna_end": null,
"cdna_length": 14753,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 74,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAH5",
"gene_hgnc_id": 2950,
"hgvs_c": "c.1105C>A",
"hgvs_p": "p.Arg369Arg",
"transcript": "XM_017009180.2",
"protein_id": "XP_016864669.1",
"transcript_support_level": null,
"aa_start": 369,
"aa_end": null,
"aa_length": 4272,
"cds_start": 1105,
"cds_end": null,
"cds_length": 12819,
"cdna_start": 1111,
"cdna_end": null,
"cdna_length": 12932,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 69,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAH5",
"gene_hgnc_id": 2950,
"hgvs_c": "c.1105C>A",
"hgvs_p": "p.Arg369Arg",
"transcript": "XM_017009181.2",
"protein_id": "XP_016864670.1",
"transcript_support_level": null,
"aa_start": 369,
"aa_end": null,
"aa_length": 3960,
"cds_start": 1105,
"cds_end": null,
"cds_length": 11883,
"cdna_start": 1111,
"cdna_end": null,
"cdna_length": 11987,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 67,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAH5",
"gene_hgnc_id": 2950,
"hgvs_c": "c.1105C>A",
"hgvs_p": "p.Arg369Arg",
"transcript": "XM_017009182.2",
"protein_id": "XP_016864671.1",
"transcript_support_level": null,
"aa_start": 369,
"aa_end": null,
"aa_length": 3809,
"cds_start": 1105,
"cds_end": null,
"cds_length": 11430,
"cdna_start": 1111,
"cdna_end": null,
"cdna_length": 11526,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 55,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAH5",
"gene_hgnc_id": 2950,
"hgvs_c": "c.1105C>A",
"hgvs_p": "p.Arg369Arg",
"transcript": "XM_017009184.2",
"protein_id": "XP_016864673.1",
"transcript_support_level": null,
"aa_start": 369,
"aa_end": null,
"aa_length": 3071,
"cds_start": 1105,
"cds_end": null,
"cds_length": 9216,
"cdna_start": 1111,
"cdna_end": null,
"cdna_length": 9297,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 49,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAH5",
"gene_hgnc_id": 2950,
"hgvs_c": "c.1105C>A",
"hgvs_p": "p.Arg369Arg",
"transcript": "XM_017009187.2",
"protein_id": "XP_016864676.1",
"transcript_support_level": null,
"aa_start": 369,
"aa_end": null,
"aa_length": 2679,
"cds_start": 1105,
"cds_end": null,
"cds_length": 8040,
"cdna_start": 1111,
"cdna_end": null,
"cdna_length": 8130,
"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": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAH5",
"gene_hgnc_id": 2950,
"hgvs_c": "n.1405C>A",
"hgvs_p": null,
"transcript": "ENST00000508040.1",
"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": 2081,
"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": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAH5",
"gene_hgnc_id": 2950,
"hgvs_c": "n.1053C>A",
"hgvs_p": null,
"transcript": "ENST00000680213.2",
"protein_id": null,
"transcript_support_level": null,
"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": 1729,
"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": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAH5",
"gene_hgnc_id": 2950,
"hgvs_c": "n.2960C>A",
"hgvs_p": null,
"transcript": "ENST00000682376.1",
"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": 7964,
"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": "DNAH5",
"gene_hgnc_id": 2950,
"hgvs_c": "n.3009C>A",
"hgvs_p": null,
"transcript": "ENST00000682586.1",
"protein_id": null,
"transcript_support_level": null,
"aa_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": 9,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAH5",
"gene_hgnc_id": 2950,
"hgvs_c": "n.936C>A",
"hgvs_p": null,
"transcript": "ENST00000683011.1",
"protein_id": null,
"transcript_support_level": null,
"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": 1595,
"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": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAH5",
"gene_hgnc_id": 2950,
"hgvs_c": "n.1096C>A",
"hgvs_p": null,
"transcript": "ENST00000683967.1",
"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,
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"cdna_length": 4015,
"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": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAH5",
"gene_hgnc_id": 2950,
"hgvs_c": "n.1096C>A",
"hgvs_p": null,
"transcript": "ENST00000684013.1",
"protein_id": null,
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"aa_start": 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": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAH5",
"gene_hgnc_id": 2950,
"hgvs_c": "n.1092C>A",
"hgvs_p": null,
"transcript": "ENST00000684099.1",
"protein_id": null,
"transcript_support_level": null,
"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": 2487,
"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": 8,
"exon_rank_end": null,
"exon_count": 54,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAH5",
"gene_hgnc_id": 2950,
"hgvs_c": "n.1111C>A",
"hgvs_p": null,
"transcript": "XR_001742034.2",
"protein_id": null,
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"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,
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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": 8,
"exon_rank_end": null,
"exon_count": 54,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAH5",
"gene_hgnc_id": 2950,
"hgvs_c": "n.1111C>A",
"hgvs_p": null,
"transcript": "XR_001742035.2",
"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": 9166,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "DNAH5",
"gene_hgnc_id": 2950,
"dbsnp": "rs771956532",
"frequency_reference_population": 0.000012394907,
"hom_count_reference_population": 0,
"allele_count_reference_population": 20,
"gnomad_exomes_af": 0.0000116318,
"gnomad_genomes_af": 0.0000197296,
"gnomad_exomes_ac": 17,
"gnomad_genomes_ac": 3,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.41999998688697815,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.09000000357627869,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.42,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.938,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.09,
"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": -5,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate,BP6_Moderate,BP7",
"acmg_by_gene": [
{
"score": -5,
"benign_score": 5,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6_Moderate",
"BP7"
],
"verdict": "Likely_benign",
"transcript": "ENST00000265104.5",
"gene_symbol": "DNAH5",
"hgnc_id": 2950,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.997C>A",
"hgvs_p": "p.Arg333Arg"
}
],
"clinvar_disease": "Primary ciliary dyskinesia",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "Primary ciliary dyskinesia",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}