← Back to variant description
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: 13-39655754-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=13&pos=39655754&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "13",
"pos": 39655754,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_020751.3",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COG6",
"gene_hgnc_id": 18621,
"hgvs_c": "c.28G>A",
"hgvs_p": "p.Ala10Thr",
"transcript": "NM_020751.3",
"protein_id": "NP_065802.1",
"transcript_support_level": null,
"aa_start": 10,
"aa_end": null,
"aa_length": 657,
"cds_start": 28,
"cds_end": null,
"cds_length": 1974,
"cdna_start": 93,
"cdna_end": null,
"cdna_length": 3574,
"mane_select": "ENST00000455146.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COG6",
"gene_hgnc_id": 18621,
"hgvs_c": "c.28G>A",
"hgvs_p": "p.Ala10Thr",
"transcript": "ENST00000455146.8",
"protein_id": "ENSP00000397441.2",
"transcript_support_level": 1,
"aa_start": 10,
"aa_end": null,
"aa_length": 657,
"cds_start": 28,
"cds_end": null,
"cds_length": 1974,
"cdna_start": 93,
"cdna_end": null,
"cdna_length": 3574,
"mane_select": "NM_020751.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COG6",
"gene_hgnc_id": 18621,
"hgvs_c": "c.28G>A",
"hgvs_p": "p.Ala10Thr",
"transcript": "ENST00000416691.6",
"protein_id": "ENSP00000403733.1",
"transcript_support_level": 1,
"aa_start": 10,
"aa_end": null,
"aa_length": 615,
"cds_start": 28,
"cds_end": null,
"cds_length": 1848,
"cdna_start": 128,
"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": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COG6",
"gene_hgnc_id": 18621,
"hgvs_c": "n.28G>A",
"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": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COG6",
"gene_hgnc_id": 18621,
"hgvs_c": "c.28G>A",
"hgvs_p": "p.Ala10Thr",
"transcript": "NM_001145079.2",
"protein_id": "NP_001138551.1",
"transcript_support_level": null,
"aa_start": 10,
"aa_end": null,
"aa_length": 615,
"cds_start": 28,
"cds_end": null,
"cds_length": 1848,
"cdna_start": 93,
"cdna_end": null,
"cdna_length": 5223,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_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": "c.28G>A",
"hgvs_p": "p.Ala10Thr",
"transcript": "ENST00000630730.1",
"protein_id": "ENSP00000486051.1",
"transcript_support_level": 5,
"aa_start": 10,
"aa_end": null,
"aa_length": 61,
"cds_start": 28,
"cds_end": null,
"cds_length": 186,
"cdna_start": 28,
"cdna_end": null,
"cdna_length": 186,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COG6",
"gene_hgnc_id": 18621,
"hgvs_c": "c.28G>A",
"hgvs_p": "p.Ala10Thr",
"transcript": "XM_011535168.2",
"protein_id": "XP_011533470.1",
"transcript_support_level": null,
"aa_start": 10,
"aa_end": null,
"aa_length": 702,
"cds_start": 28,
"cds_end": null,
"cds_length": 2109,
"cdna_start": 93,
"cdna_end": null,
"cdna_length": 3709,
"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": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COG6",
"gene_hgnc_id": 18621,
"hgvs_c": "n.93G>A",
"hgvs_p": null,
"transcript": "ENST00000422759.6",
"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": 658,
"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": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COG6",
"gene_hgnc_id": 18621,
"hgvs_c": "n.28G>A",
"hgvs_p": null,
"transcript": "ENST00000542266.5",
"protein_id": "ENSP00000441297.1",
"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": 528,
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COG6",
"gene_hgnc_id": 18621,
"hgvs_c": "n.28G>A",
"hgvs_p": null,
"transcript": "ENST00000543790.5",
"protein_id": "ENSP00000440438.1",
"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": 546,
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COG6",
"gene_hgnc_id": 18621,
"hgvs_c": "n.28G>A",
"hgvs_p": null,
"transcript": "ENST00000543804.5",
"protein_id": "ENSP00000440473.1",
"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": 553,
"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": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COG6",
"gene_hgnc_id": 18621,
"hgvs_c": "n.128G>A",
"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
}
],
"gene_symbol": "COG6",
"gene_hgnc_id": 18621,
"dbsnp": "rs3812882",
"frequency_reference_population": 0.41420677,
"hom_count_reference_population": 140263,
"allele_count_reference_population": 659307,
"gnomad_exomes_af": 0.411631,
"gnomad_genomes_af": 0.438575,
"gnomad_exomes_ac": 592562,
"gnomad_genomes_ac": 66745,
"gnomad_exomes_homalt": 125237,
"gnomad_genomes_homalt": 15026,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.000014144058695819695,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.029,
"revel_prediction": "Benign",
"alphamissense_score": 0.1002,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.6,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.101,
"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": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BA1",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "NM_020751.3",
"gene_symbol": "COG6",
"hgnc_id": 18621,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.28G>A",
"hgvs_p": "p.Ala10Thr"
}
],
"clinvar_disease": "COG6-congenital disorder of glycosylation,Hypohidrosis-enamel hypoplasia-palmoplantar keratoderma-intellectual disability syndrome,not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:8",
"phenotype_combined": "not specified|COG6-congenital disorder of glycosylation|COG6-congenital disorder of glycosylation;Hypohidrosis-enamel hypoplasia-palmoplantar keratoderma-intellectual disability syndrome|Hypohidrosis-enamel hypoplasia-palmoplantar keratoderma-intellectual disability syndrome|not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}