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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: 13-45465041-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=13&pos=45465041&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 4,
"criteria": [
"BP4_Strong"
],
"effects": [
"missense_variant"
],
"gene_symbol": "COG3",
"hgnc_id": 18619,
"hgvs_c": "c.5C>T",
"hgvs_p": "p.Ala2Val",
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -4,
"transcript": "NM_031431.4",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Strong",
"acmg_score": -4,
"allele_count_reference_population": 266,
"alphamissense_prediction": null,
"alphamissense_score": 0.5866,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.25,
"chr": "13",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.053272098302841187,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 828,
"aa_ref": "A",
"aa_start": 2,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4555,
"cdna_start": 103,
"cds_end": null,
"cds_length": 2487,
"cds_start": 5,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "NM_031431.4",
"gene_hgnc_id": 18619,
"gene_symbol": "COG3",
"hgvs_c": "c.5C>T",
"hgvs_p": "p.Ala2Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000349995.10",
"protein_coding": true,
"protein_id": "NP_113619.3",
"strand": true,
"transcript": "NM_031431.4",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 828,
"aa_ref": "A",
"aa_start": 2,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 4555,
"cdna_start": 103,
"cds_end": null,
"cds_length": 2487,
"cds_start": 5,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000349995.10",
"gene_hgnc_id": 18619,
"gene_symbol": "COG3",
"hgvs_c": "c.5C>T",
"hgvs_p": "p.Ala2Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_031431.4",
"protein_coding": true,
"protein_id": "ENSP00000258654.8",
"strand": true,
"transcript": "ENST00000349995.10",
"transcript_support_level": 1
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 444,
"aa_ref": "A",
"aa_start": 2,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1809,
"cdna_start": 37,
"cds_end": null,
"cds_length": 1335,
"cds_start": 5,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000617493.1",
"gene_hgnc_id": 18619,
"gene_symbol": "COG3",
"hgvs_c": "c.5C>T",
"hgvs_p": "p.Ala2Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000481332.1",
"strand": true,
"transcript": "ENST00000617493.1",
"transcript_support_level": 1
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 827,
"aa_ref": "A",
"aa_start": 2,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4505,
"cdna_start": 132,
"cds_end": null,
"cds_length": 2484,
"cds_start": 5,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000904057.1",
"gene_hgnc_id": 18619,
"gene_symbol": "COG3",
"hgvs_c": "c.5C>T",
"hgvs_p": "p.Ala2Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000574116.1",
"strand": true,
"transcript": "ENST00000904057.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 826,
"aa_ref": "A",
"aa_start": 2,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4467,
"cdna_start": 94,
"cds_end": null,
"cds_length": 2481,
"cds_start": 5,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000962856.1",
"gene_hgnc_id": 18619,
"gene_symbol": "COG3",
"hgvs_c": "c.5C>T",
"hgvs_p": "p.Ala2Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000632915.1",
"strand": true,
"transcript": "ENST00000962856.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 798,
"aa_ref": "A",
"aa_start": 2,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4428,
"cdna_start": 142,
"cds_end": null,
"cds_length": 2397,
"cds_start": 5,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000915269.1",
"gene_hgnc_id": 18619,
"gene_symbol": "COG3",
"hgvs_c": "c.5C>T",
"hgvs_p": "p.Ala2Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000585328.1",
"strand": true,
"transcript": "ENST00000915269.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 786,
"aa_ref": "A",
"aa_start": 2,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4388,
"cdna_start": 131,
"cds_end": null,
"cds_length": 2361,
"cds_start": 5,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000962854.1",
"gene_hgnc_id": 18619,
"gene_symbol": "COG3",
"hgvs_c": "c.5C>T",
"hgvs_p": "p.Ala2Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000632913.1",
"strand": true,
"transcript": "ENST00000962854.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 783,
"aa_ref": "A",
"aa_start": 2,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4311,
"cdna_start": 71,
"cds_end": null,
"cds_length": 2352,
"cds_start": 5,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000962857.1",
"gene_hgnc_id": 18619,
"gene_symbol": "COG3",
"hgvs_c": "c.5C>T",
"hgvs_p": "p.Ala2Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000632916.1",
"strand": true,
"transcript": "ENST00000962857.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 697,
"aa_ref": "A",
"aa_start": 2,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4086,
"cdna_start": 105,
"cds_end": null,
"cds_length": 2094,
"cds_start": 5,
"consequences": [
"missense_variant"
],
"exon_count": 20,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000962855.1",
"gene_hgnc_id": 18619,
"gene_symbol": "COG3",
"hgvs_c": "c.5C>T",
"hgvs_p": "p.Ala2Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000632914.1",
"strand": true,
"transcript": "ENST00000962855.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 390,
"aa_ref": "A",
"aa_start": 2,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3094,
"cdna_start": 27,
"cds_end": null,
"cds_length": 1173,
"cds_start": 5,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000915270.1",
"gene_hgnc_id": 18619,
"gene_symbol": "COG3",
"hgvs_c": "c.5C>T",
"hgvs_p": "p.Ala2Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000585329.1",
"strand": true,
"transcript": "ENST00000915270.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 672,
"aa_ref": "A",
"aa_start": 2,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2143,
"cdna_start": 103,
"cds_end": null,
"cds_length": 2019,
"cds_start": 5,
"consequences": [
"missense_variant"
],
"exon_count": 19,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "XM_047430702.1",
"gene_hgnc_id": 18619,
"gene_symbol": "COG3",
"hgvs_c": "c.5C>T",
"hgvs_p": "p.Ala2Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047286658.1",
"strand": true,
"transcript": "XM_047430702.1",
"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": 531,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 2,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000617325.1",
"gene_hgnc_id": 18619,
"gene_symbol": "COG3",
"hgvs_c": "n.144C>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": "ENST00000617325.1",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 1640,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 14,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "XR_007063702.1",
"gene_hgnc_id": 18619,
"gene_symbol": "COG3",
"hgvs_c": "n.103C>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": "XR_007063702.1",
"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": 4631,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 24,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "XR_429222.5",
"gene_hgnc_id": 18619,
"gene_symbol": "COG3",
"hgvs_c": "n.103C>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": "XR_429222.5",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "non_stop_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 255,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000476702.1",
"gene_hgnc_id": 18619,
"gene_symbol": "COG3",
"hgvs_c": "n.-23C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000482221.1",
"strand": true,
"transcript": "ENST00000476702.1",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 530,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 1,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000618913.1",
"gene_hgnc_id": 18619,
"gene_symbol": "COG3",
"hgvs_c": "n.-244C>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": "ENST00000618913.1",
"transcript_support_level": 6
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs760744868",
"effect": "missense_variant",
"frequency_reference_population": 0.00016927451,
"gene_hgnc_id": 18619,
"gene_symbol": "COG3",
"gnomad_exomes_ac": 252,
"gnomad_exomes_af": 0.000177569,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 14,
"gnomad_genomes_af": 0.0000919564,
"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": "Uncertain significance",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Benign",
"phylop100way_score": 2.092,
"pos": 45465041,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.203,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_031431.4"
}
]
}