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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: 19-41354715-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=41354715&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 21,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BS1",
"BS2"
],
"effects": [
"synonymous_variant"
],
"gene_symbol": "B9D2",
"hgnc_id": 28636,
"hgvs_c": "c.513C>T",
"hgvs_p": "p.Tyr171Tyr",
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -21,
"transcript": "NM_030578.4",
"verdict": "Benign"
},
{
"benign_score": 16,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS2"
],
"effects": [
"intron_variant"
],
"gene_symbol": "TMEM91",
"hgnc_id": 32393,
"hgvs_c": "c.-30+3513G>A",
"hgvs_p": null,
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -16,
"transcript": "ENST00000539627.5",
"verdict": "Benign"
},
{
"benign_score": 16,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS2"
],
"effects": [
"intron_variant"
],
"gene_symbol": "ENSG00000255730",
"hgnc_id": null,
"hgvs_c": "n.350+3513G>A",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 0,
"score": -16,
"transcript": "ENST00000604424.1",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BS1,BS2",
"acmg_score": -21,
"allele_count_reference_population": 526,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.79,
"chr": "19",
"clinvar_classification": "Benign/Likely benign",
"clinvar_disease": "Joubert syndrome,Meckel-Gruber syndrome,not specified",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:1 B:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.7900000214576721,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 175,
"aa_ref": "Y",
"aa_start": 171,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1007,
"cdna_start": 709,
"cds_end": null,
"cds_length": 528,
"cds_start": 513,
"consequences": [
"synonymous_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "NM_030578.4",
"gene_hgnc_id": 28636,
"gene_symbol": "B9D2",
"hgvs_c": "c.513C>T",
"hgvs_p": "p.Tyr171Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000243578.8",
"protein_coding": true,
"protein_id": "NP_085055.2",
"strand": false,
"transcript": "NM_030578.4",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 175,
"aa_ref": "Y",
"aa_start": 171,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 1007,
"cdna_start": 709,
"cds_end": null,
"cds_length": 528,
"cds_start": 513,
"consequences": [
"synonymous_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000243578.8",
"gene_hgnc_id": 28636,
"gene_symbol": "B9D2",
"hgvs_c": "c.513C>T",
"hgvs_p": "p.Tyr171Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_030578.4",
"protein_coding": true,
"protein_id": "ENSP00000243578.2",
"strand": false,
"transcript": "ENST00000243578.8",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 132,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1843,
"cdna_start": null,
"cds_end": null,
"cds_length": 399,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000539627.5",
"gene_hgnc_id": 32393,
"gene_symbol": "TMEM91",
"hgvs_c": "c.-30+3513G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000441900.1",
"strand": true,
"transcript": "ENST00000539627.5",
"transcript_support_level": 1
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 175,
"aa_ref": "Y",
"aa_start": 171,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 982,
"cdna_start": 684,
"cds_end": null,
"cds_length": 528,
"cds_start": 513,
"consequences": [
"synonymous_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000675972.1",
"gene_hgnc_id": 28636,
"gene_symbol": "B9D2",
"hgvs_c": "c.513C>T",
"hgvs_p": "p.Tyr171Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000501911.1",
"strand": false,
"transcript": "ENST00000675972.1",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 175,
"aa_ref": "Y",
"aa_start": 171,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1047,
"cdna_start": 754,
"cds_end": null,
"cds_length": 528,
"cds_start": 513,
"consequences": [
"synonymous_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000890351.1",
"gene_hgnc_id": 28636,
"gene_symbol": "B9D2",
"hgvs_c": "c.513C>T",
"hgvs_p": "p.Tyr171Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000560410.1",
"strand": false,
"transcript": "ENST00000890351.1",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 175,
"aa_ref": "Y",
"aa_start": 171,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 979,
"cdna_start": 688,
"cds_end": null,
"cds_length": 528,
"cds_start": 513,
"consequences": [
"synonymous_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000932334.1",
"gene_hgnc_id": 28636,
"gene_symbol": "B9D2",
"hgvs_c": "c.513C>T",
"hgvs_p": "p.Tyr171Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000602393.1",
"strand": false,
"transcript": "ENST00000932334.1",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 133,
"aa_ref": "Y",
"aa_start": 129,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 881,
"cdna_start": 583,
"cds_end": null,
"cds_length": 402,
"cds_start": 387,
"consequences": [
"synonymous_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000890348.1",
"gene_hgnc_id": 28636,
"gene_symbol": "B9D2",
"hgvs_c": "c.387C>T",
"hgvs_p": "p.Tyr129Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000560407.1",
"strand": false,
"transcript": "ENST00000890348.1",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 133,
"aa_ref": "Y",
"aa_start": 129,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 726,
"cdna_start": 431,
"cds_end": null,
"cds_length": 402,
"cds_start": 387,
"consequences": [
"synonymous_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000890350.1",
"gene_hgnc_id": 28636,
"gene_symbol": "B9D2",
"hgvs_c": "c.387C>T",
"hgvs_p": "p.Tyr129Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000560409.1",
"strand": false,
"transcript": "ENST00000890350.1",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 95,
"aa_ref": "Y",
"aa_start": 91,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 752,
"cdna_start": 459,
"cds_end": null,
"cds_length": 288,
"cds_start": 273,
"consequences": [
"synonymous_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000890349.1",
"gene_hgnc_id": 28636,
"gene_symbol": "B9D2",
"hgvs_c": "c.273C>T",
"hgvs_p": "p.Tyr91Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000560408.1",
"strand": false,
"transcript": "ENST00000890349.1",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 175,
"aa_ref": "Y",
"aa_start": 171,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 977,
"cdna_start": 679,
"cds_end": null,
"cds_length": 528,
"cds_start": 513,
"consequences": [
"synonymous_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "XM_011527349.3",
"gene_hgnc_id": 28636,
"gene_symbol": "B9D2",
"hgvs_c": "c.513C>T",
"hgvs_p": "p.Tyr171Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011525651.1",
"strand": false,
"transcript": "XM_011527349.3",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 122,
"aa_ref": "Y",
"aa_start": 118,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 915,
"cdna_start": 617,
"cds_end": null,
"cds_length": 369,
"cds_start": 354,
"consequences": [
"synonymous_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "XM_011527350.3",
"gene_hgnc_id": 28636,
"gene_symbol": "B9D2",
"hgvs_c": "c.354C>T",
"hgvs_p": "p.Tyr118Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011525652.1",
"strand": false,
"transcript": "XM_011527350.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 190,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 757,
"cdna_start": null,
"cds_end": null,
"cds_length": 573,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000604123.5",
"gene_hgnc_id": 32393,
"gene_symbol": "TMEM91",
"hgvs_c": "c.142+400G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000474871.1",
"strand": true,
"transcript": "ENST00000604123.5",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 172,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1025,
"cdna_start": null,
"cds_end": null,
"cds_length": 519,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000889861.1",
"gene_hgnc_id": 32393,
"gene_symbol": "TMEM91",
"hgvs_c": "c.-30+3513G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000559920.1",
"strand": true,
"transcript": "ENST00000889861.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 172,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 899,
"cdna_start": null,
"cds_end": null,
"cds_length": 519,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000889862.1",
"gene_hgnc_id": 32393,
"gene_symbol": "TMEM91",
"hgvs_c": "c.-30+400G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000559921.1",
"strand": true,
"transcript": "ENST00000889862.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 172,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1200,
"cdna_start": null,
"cds_end": null,
"cds_length": 519,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000966284.1",
"gene_hgnc_id": 32393,
"gene_symbol": "TMEM91",
"hgvs_c": "c.-30+1572G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000636343.1",
"strand": true,
"transcript": "ENST00000966284.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 848,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000594416.1",
"gene_hgnc_id": 28636,
"gene_symbol": "B9D2",
"hgvs_c": "n.*359C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000469666.1",
"strand": false,
"transcript": "ENST00000594416.1",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 848,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000594416.1",
"gene_hgnc_id": 28636,
"gene_symbol": "B9D2",
"hgvs_c": "n.*359C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000469666.1",
"strand": false,
"transcript": "ENST00000594416.1",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 567,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000604424.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000255730",
"hgvs_c": "n.350+3513G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000604424.1",
"transcript_support_level": 4
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs143680317",
"effect": "synonymous_variant",
"frequency_reference_population": 0.00032589395,
"gene_hgnc_id": 28636,
"gene_symbol": "B9D2",
"gnomad_exomes_ac": 488,
"gnomad_exomes_af": 0.000333854,
"gnomad_exomes_homalt": 2,
"gnomad_genomes_ac": 38,
"gnomad_genomes_af": 0.000249498,
"gnomad_genomes_homalt": 0,
"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|Joubert syndrome;Meckel-Gruber syndrome",
"phylop100way_prediction": "Benign",
"phylop100way_score": -1.059,
"pos": 41354715,
"ref": "G",
"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_030578.4"
}
]
}