← 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: 1-230675112-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=230675112&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 230675112,
"ref": "T",
"alt": "C",
"effect": "synonymous_variant",
"transcript": "ENST00000366669.9",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COG2",
"gene_hgnc_id": 6546,
"hgvs_c": "c.1014T>C",
"hgvs_p": "p.Asp338Asp",
"transcript": "NM_007357.3",
"protein_id": "NP_031383.1",
"transcript_support_level": null,
"aa_start": 338,
"aa_end": null,
"aa_length": 738,
"cds_start": 1014,
"cds_end": null,
"cds_length": 2217,
"cdna_start": 1140,
"cdna_end": null,
"cdna_length": 2932,
"mane_select": "ENST00000366669.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COG2",
"gene_hgnc_id": 6546,
"hgvs_c": "c.1014T>C",
"hgvs_p": "p.Asp338Asp",
"transcript": "ENST00000366669.9",
"protein_id": "ENSP00000355629.4",
"transcript_support_level": 1,
"aa_start": 338,
"aa_end": null,
"aa_length": 738,
"cds_start": 1014,
"cds_end": null,
"cds_length": 2217,
"cdna_start": 1140,
"cdna_end": null,
"cdna_length": 2932,
"mane_select": "NM_007357.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COG2",
"gene_hgnc_id": 6546,
"hgvs_c": "c.1014T>C",
"hgvs_p": "p.Asp338Asp",
"transcript": "ENST00000366668.7",
"protein_id": "ENSP00000355628.3",
"transcript_support_level": 1,
"aa_start": 338,
"aa_end": null,
"aa_length": 737,
"cds_start": 1014,
"cds_end": null,
"cds_length": 2214,
"cdna_start": 1054,
"cdna_end": null,
"cdna_length": 2843,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COG2",
"gene_hgnc_id": 6546,
"hgvs_c": "c.1014T>C",
"hgvs_p": "p.Asp338Asp",
"transcript": "NM_001145036.2",
"protein_id": "NP_001138508.1",
"transcript_support_level": null,
"aa_start": 338,
"aa_end": null,
"aa_length": 737,
"cds_start": 1014,
"cds_end": null,
"cds_length": 2214,
"cdna_start": 1140,
"cdna_end": null,
"cdna_length": 2929,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COG2",
"gene_hgnc_id": 6546,
"hgvs_c": "c.837T>C",
"hgvs_p": "p.Asp279Asp",
"transcript": "ENST00000534989.1",
"protein_id": "ENSP00000440349.1",
"transcript_support_level": 2,
"aa_start": 279,
"aa_end": null,
"aa_length": 679,
"cds_start": 837,
"cds_end": null,
"cds_length": 2040,
"cdna_start": 1172,
"cdna_end": null,
"cdna_length": 2963,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COG2",
"gene_hgnc_id": 6546,
"hgvs_c": "c.675T>C",
"hgvs_p": "p.Asp225Asp",
"transcript": "XM_047449445.1",
"protein_id": "XP_047305401.1",
"transcript_support_level": null,
"aa_start": 225,
"aa_end": null,
"aa_length": 625,
"cds_start": 675,
"cds_end": null,
"cds_length": 1878,
"cdna_start": 781,
"cdna_end": null,
"cdna_length": 2573,
"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": 10,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COG2",
"gene_hgnc_id": 6546,
"hgvs_c": "n.*872T>C",
"hgvs_p": null,
"transcript": "ENST00000468893.6",
"protein_id": "ENSP00000476305.1",
"transcript_support_level": 2,
"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": 2784,
"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": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COG2",
"gene_hgnc_id": 6546,
"hgvs_c": "n.3308T>C",
"hgvs_p": null,
"transcript": "ENST00000494371.5",
"protein_id": null,
"transcript_support_level": 2,
"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": 7836,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000305699",
"gene_hgnc_id": null,
"hgvs_c": "n.214A>G",
"hgvs_p": null,
"transcript": "ENST00000812487.1",
"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": 594,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000305699",
"gene_hgnc_id": null,
"hgvs_c": "n.237A>G",
"hgvs_p": null,
"transcript": "ENST00000812490.1",
"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": 409,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LOC107985358",
"gene_hgnc_id": null,
"hgvs_c": "n.187A>G",
"hgvs_p": null,
"transcript": "XR_001738517.1",
"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": 354,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COG2",
"gene_hgnc_id": 6546,
"hgvs_c": "n.*872T>C",
"hgvs_p": null,
"transcript": "ENST00000468893.6",
"protein_id": "ENSP00000476305.1",
"transcript_support_level": 2,
"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": 2784,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "COG2",
"gene_hgnc_id": 6546,
"dbsnp": "rs113173809",
"frequency_reference_population": 0.005707223,
"hom_count_reference_population": 36,
"allele_count_reference_population": 9198,
"gnomad_exomes_af": 0.00587606,
"gnomad_genomes_af": 0.00408981,
"gnomad_exomes_ac": 8575,
"gnomad_genomes_ac": 623,
"gnomad_exomes_homalt": 33,
"gnomad_genomes_homalt": 3,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.6000000238418579,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"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": -0.6,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.822,
"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": -21,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BS1,BS2",
"acmg_by_gene": [
{
"score": -21,
"benign_score": 21,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000366669.9",
"gene_symbol": "COG2",
"hgnc_id": 6546,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1014T>C",
"hgvs_p": "p.Asp338Asp"
},
{
"score": -16,
"benign_score": 16,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000812487.1",
"gene_symbol": "ENSG00000305699",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.214A>G",
"hgvs_p": null
},
{
"score": -16,
"benign_score": 16,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS2"
],
"verdict": "Benign",
"transcript": "XR_001738517.1",
"gene_symbol": "LOC107985358",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.187A>G",
"hgvs_p": null
}
],
"clinvar_disease": " type IIq,COG2-related disorder,Congenital disorder of glycosylation,not provided",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:1 B:2",
"phenotype_combined": "Congenital disorder of glycosylation, type IIq|not provided|COG2-related disorder",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}