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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: 17-7580783-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=7580783&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM2"
],
"effects": [
"stop_gained",
"splice_region_variant"
],
"gene_symbol": "CD68",
"hgnc_id": 1693,
"hgvs_c": "c.760C>T",
"hgvs_p": "p.Gln254*",
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": 2,
"transcript": "NM_001251.3",
"verdict": "Uncertain_significance"
},
{
"benign_score": 0,
"criteria": [
"PM2",
"PP3_Moderate"
],
"effects": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"gene_symbol": "ENSG00000264772",
"hgnc_id": null,
"hgvs_c": "n.3736C>T",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 4,
"score": 4,
"transcript": "ENST00000581621.1",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_score": 2,
"allele_count_reference_population": 5,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.33,
"chr": "17",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.33000001311302185,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 354,
"aa_ref": "Q",
"aa_start": 254,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1705,
"cdna_start": 800,
"cds_end": null,
"cds_length": 1065,
"cds_start": 760,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_count": 6,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "NM_001251.3",
"gene_hgnc_id": 1693,
"gene_symbol": "CD68",
"hgvs_c": "c.760C>T",
"hgvs_p": "p.Gln254*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000250092.11",
"protein_coding": true,
"protein_id": "NP_001242.2",
"strand": true,
"transcript": "NM_001251.3",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 354,
"aa_ref": "Q",
"aa_start": 254,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 1705,
"cdna_start": 800,
"cds_end": null,
"cds_length": 1065,
"cds_start": 760,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_count": 6,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000250092.11",
"gene_hgnc_id": 1693,
"gene_symbol": "CD68",
"hgvs_c": "c.760C>T",
"hgvs_p": "p.Gln254*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001251.3",
"protein_coding": true,
"protein_id": "ENSP00000250092.6",
"strand": true,
"transcript": "ENST00000250092.11",
"transcript_support_level": 1
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 327,
"aa_ref": "Q",
"aa_start": 227,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1771,
"cdna_start": 866,
"cds_end": null,
"cds_length": 984,
"cds_start": 679,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_count": 6,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000380498.10",
"gene_hgnc_id": 1693,
"gene_symbol": "CD68",
"hgvs_c": "c.679C>T",
"hgvs_p": "p.Gln227*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000369867.6",
"strand": true,
"transcript": "ENST00000380498.10",
"transcript_support_level": 1
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 327,
"aa_ref": "Q",
"aa_start": 227,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1624,
"cdna_start": 719,
"cds_end": null,
"cds_length": 984,
"cds_start": 679,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_count": 6,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "NM_001040059.2",
"gene_hgnc_id": 1693,
"gene_symbol": "CD68",
"hgvs_c": "c.679C>T",
"hgvs_p": "p.Gln227*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001035148.1",
"strand": true,
"transcript": "NM_001040059.2",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 321,
"aa_ref": "P",
"aa_start": 254,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1622,
"cdna_start": 816,
"cds_end": null,
"cds_length": 966,
"cds_start": 760,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 6,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000852832.1",
"gene_hgnc_id": 1693,
"gene_symbol": "CD68",
"hgvs_c": "c.760C>T",
"hgvs_p": "p.Pro254Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000522891.1",
"strand": true,
"transcript": "ENST00000852832.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 314,
"aa_ref": "Q",
"aa_start": 214,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1844,
"cdna_start": 938,
"cds_end": null,
"cds_length": 945,
"cds_start": 640,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_count": 5,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000965359.1",
"gene_hgnc_id": 1693,
"gene_symbol": "CD68",
"hgvs_c": "c.640C>T",
"hgvs_p": "p.Gln214*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000635418.1",
"strand": true,
"transcript": "ENST00000965359.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 297,
"aa_ref": "R",
"aa_start": 254,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1544,
"cdna_start": 811,
"cds_end": null,
"cds_length": 894,
"cds_start": 760,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 5,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000965360.1",
"gene_hgnc_id": 1693,
"gene_symbol": "CD68",
"hgvs_c": "c.760C>T",
"hgvs_p": "p.Arg254Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000635419.1",
"strand": true,
"transcript": "ENST00000965360.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 120,
"aa_ref": "Q",
"aa_start": 55,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 891,
"cdna_start": 164,
"cds_end": null,
"cds_length": 363,
"cds_start": 163,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_count": 3,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000584180.1",
"gene_hgnc_id": 1693,
"gene_symbol": "CD68",
"hgvs_c": "c.163C>T",
"hgvs_p": "p.Gln55*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000462198.1",
"strand": true,
"transcript": "ENST00000584180.1",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 4554,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_count": 12,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000581621.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000264772",
"hgvs_c": "n.3736C>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": "ENST00000581621.1",
"transcript_support_level": 2
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": "Benign",
"dbscsnv_ada_score": 0.0012084397311145,
"dbsnp": "rs9901673",
"effect": "stop_gained,splice_region_variant",
"frequency_reference_population": 0.0000030984886,
"gene_hgnc_id": 1693,
"gene_symbol": "CD68",
"gnomad_exomes_ac": 3,
"gnomad_exomes_af": 0.00000205224,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 2,
"gnomad_genomes_af": 0.0000131692,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": null,
"phenotype_combined": null,
"phylop100way_prediction": "Benign",
"phylop100way_score": 0.846,
"pos": 7580783,
"ref": "C",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.09399999678134918,
"splice_source_selected": "dbscSNV1_RF",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.02,
"transcript": "NM_001251.3"
}
]
}