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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: 19-36017450-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=36017450&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 5,
"criteria": [
"PM2",
"BP4_Moderate",
"BP6_Moderate",
"BP7"
],
"effects": [
"splice_region_variant",
"synonymous_variant"
],
"gene_symbol": "CLIP3",
"hgnc_id": 24314,
"hgvs_c": "c.1452G>A",
"hgvs_p": "p.Arg484Arg",
"inheritance_mode": "AD",
"pathogenic_score": 2,
"score": -3,
"transcript": "NM_015526.3",
"verdict": "Likely_benign"
},
{
"benign_score": 4,
"criteria": [
"PM2",
"BP4_Moderate",
"BP6_Moderate"
],
"effects": [
"intron_variant"
],
"gene_symbol": "ENSG00000267698",
"hgnc_id": null,
"hgvs_c": "n.228+490C>T",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 2,
"score": -2,
"transcript": "ENST00000586962.1",
"verdict": "Likely_benign"
},
{
"benign_score": 4,
"criteria": [
"PM2",
"BP4_Moderate",
"BP6_Moderate"
],
"effects": [
"intron_variant"
],
"gene_symbol": "LOC101927572",
"hgnc_id": null,
"hgvs_c": "n.234+490C>T",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 2,
"score": -2,
"transcript": "NR_170987.1",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Moderate,BP6_Moderate,BP7",
"acmg_score": -3,
"allele_count_reference_population": 0,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.36,
"chr": "19",
"clinvar_classification": "Likely benign",
"clinvar_disease": "not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.36000001430511475,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 547,
"aa_ref": "R",
"aa_start": 484,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3350,
"cdna_start": 1660,
"cds_end": null,
"cds_length": 1644,
"cds_start": 1452,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_count": 14,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "NM_015526.3",
"gene_hgnc_id": 24314,
"gene_symbol": "CLIP3",
"hgvs_c": "c.1452G>A",
"hgvs_p": "p.Arg484Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000360535.9",
"protein_coding": true,
"protein_id": "NP_056341.1",
"strand": false,
"transcript": "NM_015526.3",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 547,
"aa_ref": "R",
"aa_start": 484,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 3350,
"cdna_start": 1660,
"cds_end": null,
"cds_length": 1644,
"cds_start": 1452,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_count": 14,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000360535.9",
"gene_hgnc_id": 24314,
"gene_symbol": "CLIP3",
"hgvs_c": "c.1452G>A",
"hgvs_p": "p.Arg484Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_015526.3",
"protein_coding": true,
"protein_id": "ENSP00000353732.3",
"strand": false,
"transcript": "ENST00000360535.9",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 643,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000586962.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000267698",
"hgvs_c": "n.228+490C>T",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000586962.1",
"transcript_support_level": 1
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 547,
"aa_ref": "R",
"aa_start": 484,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3420,
"cdna_start": 1730,
"cds_end": null,
"cds_length": 1644,
"cds_start": 1452,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_count": 13,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "NM_001199570.2",
"gene_hgnc_id": 24314,
"gene_symbol": "CLIP3",
"hgvs_c": "c.1452G>A",
"hgvs_p": "p.Arg484Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001186499.1",
"strand": false,
"transcript": "NM_001199570.2",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 547,
"aa_ref": "R",
"aa_start": 484,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2080,
"cdna_start": 1766,
"cds_end": null,
"cds_length": 1644,
"cds_start": 1452,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_count": 13,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000593074.5",
"gene_hgnc_id": 24314,
"gene_symbol": "CLIP3",
"hgvs_c": "c.1452G>A",
"hgvs_p": "p.Arg484Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000466832.1",
"strand": false,
"transcript": "ENST00000593074.5",
"transcript_support_level": 2
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 547,
"aa_ref": "R",
"aa_start": 484,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3300,
"cdna_start": 1610,
"cds_end": null,
"cds_length": 1644,
"cds_start": 1452,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_count": 14,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000904679.1",
"gene_hgnc_id": 24314,
"gene_symbol": "CLIP3",
"hgvs_c": "c.1452G>A",
"hgvs_p": "p.Arg484Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000574738.1",
"strand": false,
"transcript": "ENST00000904679.1",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 547,
"aa_ref": "R",
"aa_start": 484,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2177,
"cdna_start": 1556,
"cds_end": null,
"cds_length": 1644,
"cds_start": 1452,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_count": 14,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000904680.1",
"gene_hgnc_id": 24314,
"gene_symbol": "CLIP3",
"hgvs_c": "c.1452G>A",
"hgvs_p": "p.Arg484Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000574739.1",
"strand": false,
"transcript": "ENST00000904680.1",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 504,
"aa_ref": "R",
"aa_start": 441,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3201,
"cdna_start": 1512,
"cds_end": null,
"cds_length": 1515,
"cds_start": 1323,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_count": 13,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000923666.1",
"gene_hgnc_id": 24314,
"gene_symbol": "CLIP3",
"hgvs_c": "c.1323G>A",
"hgvs_p": "p.Arg441Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000593725.1",
"strand": false,
"transcript": "ENST00000923666.1",
"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": 538,
"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": "ENST00000685157.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000267698",
"hgvs_c": "n.243+490C>T",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000685157.1",
"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": 634,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000718825.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000267698",
"hgvs_c": "n.190+490C>T",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000718825.1",
"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": 515,
"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": "ENST00000718826.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000267698",
"hgvs_c": "n.80-1784C>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": "ENST00000718826.1",
"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": 669,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000718827.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000267698",
"hgvs_c": "n.220+490C>T",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000718827.1",
"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": 1024,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NR_170987.1",
"gene_hgnc_id": null,
"gene_symbol": "LOC101927572",
"hgvs_c": "n.234+490C>T",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "NR_170987.1",
"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": 678,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NR_170988.1",
"gene_hgnc_id": null,
"gene_symbol": "LOC101927572",
"hgvs_c": "n.234+490C>T",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "NR_170988.1",
"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": 555,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000718828.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000267698",
"hgvs_c": "n.*136C>T",
"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": "ENST00000718828.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": "Benign",
"dbscsnv_ada_score": 0.0208803488075775,
"dbsnp": null,
"effect": "splice_region_variant,synonymous_variant",
"frequency_reference_population": null,
"gene_hgnc_id": 24314,
"gene_symbol": "CLIP3",
"gnomad_exomes_ac": null,
"gnomad_exomes_af": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Likely benign",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Benign",
"phylop100way_score": 0.397,
"pos": 36017450,
"ref": "C",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.20800000429153442,
"splice_source_selected": "dbscSNV1_RF",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_015526.3"
}
]
}