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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: 5-13752284-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=13752284&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 11,
"criteria": [
"BP4_Moderate",
"BP6_Very_Strong",
"BP7"
],
"effects": [
"synonymous_variant"
],
"gene_symbol": "DNAH5",
"hgnc_id": 2950,
"hgvs_c": "c.10878G>A",
"hgvs_p": "p.Thr3626Thr",
"inheritance_mode": "AD,AR",
"pathogenic_score": 0,
"score": -11,
"transcript": "NM_001369.3",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Moderate,BP6_Very_Strong,BP7",
"acmg_score": -11,
"allele_count_reference_population": 103,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.42,
"chr": "5",
"clinvar_classification": "Benign/Likely benign",
"clinvar_disease": "Primary ciliary dyskinesia,Primary ciliary dyskinesia 3,not specified",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:3 B:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.41999998688697815,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 4624,
"aa_ref": "T",
"aa_start": 3626,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 15781,
"cdna_start": 11128,
"cds_end": null,
"cds_length": 13875,
"cds_start": 10878,
"consequences": [
"synonymous_variant"
],
"exon_count": 79,
"exon_rank": 64,
"exon_rank_end": null,
"feature": "NM_001369.3",
"gene_hgnc_id": 2950,
"gene_symbol": "DNAH5",
"hgvs_c": "c.10878G>A",
"hgvs_p": "p.Thr3626Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000265104.5",
"protein_coding": true,
"protein_id": "NP_001360.1",
"strand": false,
"transcript": "NM_001369.3",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 4624,
"aa_ref": "T",
"aa_start": 3626,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 15781,
"cdna_start": 11128,
"cds_end": null,
"cds_length": 13875,
"cds_start": 10878,
"consequences": [
"synonymous_variant"
],
"exon_count": 79,
"exon_rank": 64,
"exon_rank_end": null,
"feature": "ENST00000265104.5",
"gene_hgnc_id": 2950,
"gene_symbol": "DNAH5",
"hgvs_c": "c.10878G>A",
"hgvs_p": "p.Thr3626Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001369.3",
"protein_coding": true,
"protein_id": "ENSP00000265104.4",
"strand": false,
"transcript": "ENST00000265104.5",
"transcript_support_level": 1
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 4609,
"aa_ref": "T",
"aa_start": 3611,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 15645,
"cdna_start": 10992,
"cds_end": null,
"cds_length": 13830,
"cds_start": 10833,
"consequences": [
"synonymous_variant"
],
"exon_count": 79,
"exon_rank": 64,
"exon_rank_end": null,
"feature": "ENST00000681290.1",
"gene_hgnc_id": 2950,
"gene_symbol": "DNAH5",
"hgvs_c": "c.10833G>A",
"hgvs_p": "p.Thr3611Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000505288.1",
"strand": false,
"transcript": "ENST00000681290.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 4660,
"aa_ref": "T",
"aa_start": 3662,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 15645,
"cdna_start": 10992,
"cds_end": null,
"cds_length": 13983,
"cds_start": 10986,
"consequences": [
"synonymous_variant"
],
"exon_count": 79,
"exon_rank": 64,
"exon_rank_end": null,
"feature": "XM_005248262.4",
"gene_hgnc_id": 2950,
"gene_symbol": "DNAH5",
"hgvs_c": "c.10986G>A",
"hgvs_p": "p.Thr3662Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_005248319.2",
"strand": false,
"transcript": "XM_005248262.4",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 4544,
"aa_ref": "T",
"aa_start": 3546,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 16410,
"cdna_start": 11757,
"cds_end": null,
"cds_length": 13635,
"cds_start": 10638,
"consequences": [
"synonymous_variant"
],
"exon_count": 79,
"exon_rank": 64,
"exon_rank_end": null,
"feature": "XM_047416886.1",
"gene_hgnc_id": 2950,
"gene_symbol": "DNAH5",
"hgvs_c": "c.10638G>A",
"hgvs_p": "p.Thr3546Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047272842.1",
"strand": false,
"transcript": "XM_047416886.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 4520,
"aa_ref": "T",
"aa_start": 3662,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 15225,
"cdna_start": 10992,
"cds_end": null,
"cds_length": 13563,
"cds_start": 10986,
"consequences": [
"synonymous_variant"
],
"exon_count": 77,
"exon_rank": 64,
"exon_rank_end": null,
"feature": "XM_017009177.2",
"gene_hgnc_id": 2950,
"gene_symbol": "DNAH5",
"hgvs_c": "c.10986G>A",
"hgvs_p": "p.Thr3662Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016864666.1",
"strand": false,
"transcript": "XM_017009177.2",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 4295,
"aa_ref": "T",
"aa_start": 3297,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 14753,
"cdna_start": 10100,
"cds_end": null,
"cds_length": 12888,
"cds_start": 9891,
"consequences": [
"synonymous_variant"
],
"exon_count": 73,
"exon_rank": 58,
"exon_rank_end": null,
"feature": "XM_017009179.3",
"gene_hgnc_id": 2950,
"gene_symbol": "DNAH5",
"hgvs_c": "c.9891G>A",
"hgvs_p": "p.Thr3297Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016864668.1",
"strand": false,
"transcript": "XM_017009179.3",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 4272,
"aa_ref": "T",
"aa_start": 3662,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 12932,
"cdna_start": 10992,
"cds_end": null,
"cds_length": 12819,
"cds_start": 10986,
"consequences": [
"synonymous_variant"
],
"exon_count": 74,
"exon_rank": 64,
"exon_rank_end": null,
"feature": "XM_017009180.2",
"gene_hgnc_id": 2950,
"gene_symbol": "DNAH5",
"hgvs_c": "c.10986G>A",
"hgvs_p": "p.Thr3662Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016864669.1",
"strand": false,
"transcript": "XM_017009180.2",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 3960,
"aa_ref": "T",
"aa_start": 3662,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 11987,
"cdna_start": 10992,
"cds_end": null,
"cds_length": 11883,
"cds_start": 10986,
"consequences": [
"synonymous_variant"
],
"exon_count": 69,
"exon_rank": 64,
"exon_rank_end": null,
"feature": "XM_017009181.2",
"gene_hgnc_id": 2950,
"gene_symbol": "DNAH5",
"hgvs_c": "c.10986G>A",
"hgvs_p": "p.Thr3662Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016864670.1",
"strand": false,
"transcript": "XM_017009181.2",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 3809,
"aa_ref": "T",
"aa_start": 3662,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 11526,
"cdna_start": 10992,
"cds_end": null,
"cds_length": 11430,
"cds_start": 10986,
"consequences": [
"synonymous_variant"
],
"exon_count": 67,
"exon_rank": 64,
"exon_rank_end": null,
"feature": "XM_017009182.2",
"gene_hgnc_id": 2950,
"gene_symbol": "DNAH5",
"hgvs_c": "c.10986G>A",
"hgvs_p": "p.Thr3662Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016864671.1",
"strand": false,
"transcript": "XM_017009182.2",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 3023,
"aa_ref": "T",
"aa_start": 2025,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 10952,
"cdna_start": 6299,
"cds_end": null,
"cds_length": 9072,
"cds_start": 6075,
"consequences": [
"synonymous_variant"
],
"exon_count": 51,
"exon_rank": 36,
"exon_rank_end": null,
"feature": "XM_017009185.1",
"gene_hgnc_id": 2950,
"gene_symbol": "DNAH5",
"hgvs_c": "c.6075G>A",
"hgvs_p": "p.Thr2025Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016864674.1",
"strand": false,
"transcript": "XM_017009185.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 2874,
"aa_ref": "T",
"aa_start": 1876,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 10383,
"cdna_start": 5730,
"cds_end": null,
"cds_length": 8625,
"cds_start": 5628,
"consequences": [
"synonymous_variant"
],
"exon_count": 48,
"exon_rank": 33,
"exon_rank_end": null,
"feature": "XM_017009186.2",
"gene_hgnc_id": 2950,
"gene_symbol": "DNAH5",
"hgvs_c": "c.5628G>A",
"hgvs_p": "p.Thr1876Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016864675.1",
"strand": false,
"transcript": "XM_017009186.2",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 2653,
"aa_ref": "T",
"aa_start": 1655,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 11185,
"cdna_start": 6532,
"cds_end": null,
"cds_length": 7962,
"cds_start": 4965,
"consequences": [
"synonymous_variant"
],
"exon_count": 45,
"exon_rank": 30,
"exon_rank_end": null,
"feature": "XM_017009188.2",
"gene_hgnc_id": 2950,
"gene_symbol": "DNAH5",
"hgvs_c": "c.4965G>A",
"hgvs_p": "p.Thr1655Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016864677.1",
"strand": false,
"transcript": "XM_017009188.2",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs188428209",
"effect": "synonymous_variant",
"frequency_reference_population": 0.000063817395,
"gene_hgnc_id": 2950,
"gene_symbol": "DNAH5",
"gnomad_exomes_ac": 95,
"gnomad_exomes_af": 0.0000649922,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_ac": 8,
"gnomad_genomes_af": 0.0000525396,
"gnomad_genomes_homalt": 1,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 2,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Benign/Likely benign",
"phenotype_combined": "not specified|Primary ciliary dyskinesia|Primary ciliary dyskinesia 3",
"phylop100way_prediction": "Benign",
"phylop100way_score": -0.437,
"pos": 13752284,
"ref": "C",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_001369.3"
}
]
}