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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: 6-35499990-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=35499990&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 5,
"criteria": [
"PM1",
"PP2",
"BP4_Strong",
"BP6"
],
"effects": [
"missense_variant"
],
"gene_symbol": "TULP1",
"hgnc_id": 12423,
"hgvs_c": "c.1486G>A",
"hgvs_p": "p.Ala496Thr",
"inheritance_mode": "AD,AR",
"pathogenic_score": 3,
"score": -2,
"transcript": "NM_003322.6",
"verdict": "Likely_benign"
},
{
"benign_score": 5,
"criteria": [
"BP4_Strong",
"BP6"
],
"effects": [
"intron_variant"
],
"gene_symbol": "LINC03135",
"hgnc_id": 58100,
"hgvs_c": "n.121+2263C>T",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 0,
"score": -5,
"transcript": "ENST00000722033.1",
"verdict": "Likely_benign"
},
{
"benign_score": 5,
"criteria": [
"BP4_Strong",
"BP6"
],
"effects": [
"intron_variant"
],
"gene_symbol": "LOC124901309",
"hgnc_id": null,
"hgvs_c": "n.75+1783C>T",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 0,
"score": -5,
"transcript": "XR_007059561.1",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM1,PP2,BP4_Strong,BP6",
"acmg_score": -2,
"allele_count_reference_population": 1149,
"alphamissense_prediction": null,
"alphamissense_score": 0.0971,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.33,
"chr": "6",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_disease": "Leber congenital amaurosis 15,Retinitis pigmentosa,TULP1-related disorder,not provided,not specified",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:3 LB:2 B:1 O:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.008816510438919067,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 542,
"aa_ref": "A",
"aa_start": 496,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2120,
"cdna_start": 1524,
"cds_end": null,
"cds_length": 1629,
"cds_start": 1486,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "NM_003322.6",
"gene_hgnc_id": 12423,
"gene_symbol": "TULP1",
"hgvs_c": "c.1486G>A",
"hgvs_p": "p.Ala496Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000229771.11",
"protein_coding": true,
"protein_id": "NP_003313.3",
"strand": false,
"transcript": "NM_003322.6",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 542,
"aa_ref": "A",
"aa_start": 496,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2120,
"cdna_start": 1524,
"cds_end": null,
"cds_length": 1629,
"cds_start": 1486,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "ENST00000229771.11",
"gene_hgnc_id": 12423,
"gene_symbol": "TULP1",
"hgvs_c": "c.1486G>A",
"hgvs_p": "p.Ala496Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_003322.6",
"protein_coding": true,
"protein_id": "ENSP00000229771.6",
"strand": false,
"transcript": "ENST00000229771.11",
"transcript_support_level": 1
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 489,
"aa_ref": "A",
"aa_start": 443,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1941,
"cdna_start": 1345,
"cds_end": null,
"cds_length": 1470,
"cds_start": 1327,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000322263.8",
"gene_hgnc_id": 12423,
"gene_symbol": "TULP1",
"hgvs_c": "c.1327G>A",
"hgvs_p": "p.Ala443Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000319414.4",
"strand": false,
"transcript": "ENST00000322263.8",
"transcript_support_level": 1
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 540,
"aa_ref": "A",
"aa_start": 494,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2084,
"cdna_start": 1491,
"cds_end": null,
"cds_length": 1623,
"cds_start": 1480,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000614066.4",
"gene_hgnc_id": 12423,
"gene_symbol": "TULP1",
"hgvs_c": "c.1480G>A",
"hgvs_p": "p.Ala494Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000477534.1",
"strand": false,
"transcript": "ENST00000614066.4",
"transcript_support_level": 5
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 489,
"aa_ref": "A",
"aa_start": 443,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1961,
"cdna_start": 1365,
"cds_end": null,
"cds_length": 1470,
"cds_start": 1327,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "NM_001289395.2",
"gene_hgnc_id": 12423,
"gene_symbol": "TULP1",
"hgvs_c": "c.1327G>A",
"hgvs_p": "p.Ala443Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001276324.1",
"strand": false,
"transcript": "NM_001289395.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 644,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000722033.1",
"gene_hgnc_id": 58100,
"gene_symbol": "LINC03135",
"hgvs_c": "n.121+2263C>T",
"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": "ENST00000722033.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 509,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000722034.1",
"gene_hgnc_id": 58100,
"gene_symbol": "LINC03135",
"hgvs_c": "n.124+2263C>T",
"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": "ENST00000722034.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 473,
"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": "ENST00000722035.1",
"gene_hgnc_id": 58100,
"gene_symbol": "LINC03135",
"hgvs_c": "n.203+2263C>T",
"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": "ENST00000722035.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 505,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000722036.1",
"gene_hgnc_id": 58100,
"gene_symbol": "LINC03135",
"hgvs_c": "n.116+2263C>T",
"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": "ENST00000722036.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 471,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000722037.1",
"gene_hgnc_id": 58100,
"gene_symbol": "LINC03135",
"hgvs_c": "n.113+2263C>T",
"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": "ENST00000722037.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 855,
"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": "ENST00000722038.1",
"gene_hgnc_id": 58100,
"gene_symbol": "LINC03135",
"hgvs_c": "n.586+1783C>T",
"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": "ENST00000722038.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 343,
"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": "XR_007059561.1",
"gene_hgnc_id": null,
"gene_symbol": "LOC124901309",
"hgvs_c": "n.75+1783C>T",
"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": "XR_007059561.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 582,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000495781.1",
"gene_hgnc_id": 12423,
"gene_symbol": "TULP1",
"hgvs_c": "n.*80G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000495781.1",
"transcript_support_level": 3
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs141980901",
"effect": "missense_variant",
"frequency_reference_population": 0.00071187917,
"gene_hgnc_id": 12423,
"gene_symbol": "TULP1",
"gnomad_exomes_ac": 985,
"gnomad_exomes_af": 0.00067384,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 164,
"gnomad_genomes_af": 0.00107706,
"gnomad_genomes_homalt": 1,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 1,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"phenotype_combined": "not provided|Retinitis pigmentosa|Leber congenital amaurosis 15|not specified|TULP1-related disorder",
"phylop100way_prediction": "Benign",
"phylop100way_score": -0.083,
"pos": 35499990,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.162,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_003322.6"
}
]
}