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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: 13-39679963-A-AT (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=13&pos=39679963&ref=A&alt=AT&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "13",
"pos": 39679963,
"ref": "A",
"alt": "AT",
"effect": "splice_acceptor_variant,intron_variant",
"transcript": "ENST00000455146.8",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "COG6",
"gene_hgnc_id": 18621,
"hgvs_c": "c.624-3dupT",
"hgvs_p": null,
"transcript": "NM_020751.3",
"protein_id": "NP_065802.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 657,
"cds_start": -4,
"cds_end": null,
"cds_length": 1974,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3574,
"mane_select": "ENST00000455146.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "COG6",
"gene_hgnc_id": 18621,
"hgvs_c": "c.624-3dupT",
"hgvs_p": null,
"transcript": "ENST00000455146.8",
"protein_id": "ENSP00000397441.2",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 657,
"cds_start": -4,
"cds_end": null,
"cds_length": 1974,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3574,
"mane_select": "NM_020751.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "COG6",
"gene_hgnc_id": 18621,
"hgvs_c": "c.624-3dupT",
"hgvs_p": null,
"transcript": "ENST00000416691.6",
"protein_id": "ENSP00000403733.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 615,
"cds_start": -4,
"cds_end": null,
"cds_length": 1848,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5258,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "COG6",
"gene_hgnc_id": 18621,
"hgvs_c": "n.*461-3dupT",
"hgvs_p": null,
"transcript": "ENST00000356576.8",
"protein_id": "ENSP00000348983.4",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3449,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COG6",
"gene_hgnc_id": 18621,
"hgvs_c": "n.377dupT",
"hgvs_p": null,
"transcript": "ENST00000465775.1",
"protein_id": null,
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 753,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "COG6",
"gene_hgnc_id": 18621,
"hgvs_c": "c.624-3dupT",
"hgvs_p": null,
"transcript": "NM_001145079.2",
"protein_id": "NP_001138551.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 615,
"cds_start": -4,
"cds_end": null,
"cds_length": 1848,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5223,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "COG6",
"gene_hgnc_id": 18621,
"hgvs_c": "n.355-3dupT",
"hgvs_p": null,
"transcript": "ENST00000536488.5",
"protein_id": "ENSP00000445217.1",
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 564,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "COG6",
"gene_hgnc_id": 18621,
"hgvs_c": "n.275-3dupT",
"hgvs_p": null,
"transcript": "ENST00000537156.1",
"protein_id": null,
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 530,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "COG6",
"gene_hgnc_id": 18621,
"hgvs_c": "n.789-3dupT",
"hgvs_p": null,
"transcript": "NR_026745.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3674,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "COG6",
"gene_hgnc_id": 18621,
"hgvs_c": "c.624-3dupT",
"hgvs_p": null,
"transcript": "XM_011535168.2",
"protein_id": "XP_011533470.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 702,
"cds_start": -4,
"cds_end": null,
"cds_length": 2109,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3709,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "COG6",
"gene_hgnc_id": 18621,
"dbsnp": "rs397756552",
"frequency_reference_population": 0.23564269,
"hom_count_reference_population": 35440,
"allele_count_reference_population": 327393,
"gnomad_exomes_af": 0.231001,
"gnomad_genomes_af": 0.273562,
"gnomad_exomes_ac": 285939,
"gnomad_genomes_ac": 41454,
"gnomad_exomes_homalt": 29582,
"gnomad_genomes_homalt": 5858,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": -0.428,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -14,
"acmg_classification": "Benign",
"acmg_criteria": "PVS1_Moderate,BP6_Very_Strong,BA1",
"acmg_by_gene": [
{
"score": -14,
"benign_score": 16,
"pathogenic_score": 2,
"criteria": [
"PVS1_Moderate",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000455146.8",
"gene_symbol": "COG6",
"hgnc_id": 18621,
"effects": [
"splice_acceptor_variant",
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.624-3dupT",
"hgvs_p": null
}
],
"clinvar_disease": "COG6-congenital disorder of glycosylation,Congenital disorder of glycosylation,Hypohidrosis-enamel hypoplasia-palmoplantar keratoderma-intellectual disability syndrome,not provided,not specified",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:1 B:4",
"phenotype_combined": "not specified|Congenital disorder of glycosylation|not provided|COG6-congenital disorder of glycosylation;Hypohidrosis-enamel hypoplasia-palmoplantar keratoderma-intellectual disability syndrome",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}