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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: 8-99274325-A-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=8&pos=99274325&ref=A&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "8",
"pos": 99274325,
"ref": "A",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_017890.5",
"consequences": [
{
"aa_ref": "K",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 62,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS13B",
"gene_hgnc_id": 2183,
"hgvs_c": "c.2643A>T",
"hgvs_p": "p.Lys881Asn",
"transcript": "NM_017890.5",
"protein_id": "NP_060360.3",
"transcript_support_level": null,
"aa_start": 881,
"aa_end": null,
"aa_length": 4022,
"cds_start": 2643,
"cds_end": null,
"cds_length": 12069,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": "ENST00000358544.7",
"biotype": "protein_coding",
"feature": "NM_017890.5"
},
{
"aa_ref": "K",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 62,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS13B",
"gene_hgnc_id": 2183,
"hgvs_c": "c.2643A>T",
"hgvs_p": "p.Lys881Asn",
"transcript": "ENST00000358544.7",
"protein_id": "ENSP00000351346.2",
"transcript_support_level": 1,
"aa_start": 881,
"aa_end": null,
"aa_length": 4022,
"cds_start": 2643,
"cds_end": null,
"cds_length": 12069,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": "NM_017890.5",
"biotype": "protein_coding",
"feature": "ENST00000358544.7"
},
{
"aa_ref": "K",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 62,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS13B",
"gene_hgnc_id": 2183,
"hgvs_c": "c.2643A>T",
"hgvs_p": "p.Lys881Asn",
"transcript": "NM_152564.5",
"protein_id": "NP_689777.3",
"transcript_support_level": null,
"aa_start": 881,
"aa_end": null,
"aa_length": 3997,
"cds_start": 2643,
"cds_end": null,
"cds_length": 11994,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000357162.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_152564.5"
},
{
"aa_ref": "K",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 62,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS13B",
"gene_hgnc_id": 2183,
"hgvs_c": "c.2643A>T",
"hgvs_p": "p.Lys881Asn",
"transcript": "ENST00000357162.7",
"protein_id": "ENSP00000349685.2",
"transcript_support_level": 1,
"aa_start": 881,
"aa_end": null,
"aa_length": 3997,
"cds_start": 2643,
"cds_end": null,
"cds_length": 11994,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_152564.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000357162.7"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS13B",
"gene_hgnc_id": 2183,
"hgvs_c": "n.2643A>T",
"hgvs_p": null,
"transcript": "ENST00000355155.6",
"protein_id": "ENSP00000347281.2",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000355155.6"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS13B",
"gene_hgnc_id": 2183,
"hgvs_c": "n.2643A>T",
"hgvs_p": null,
"transcript": "ENST00000496144.5",
"protein_id": "ENSP00000430900.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000496144.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS13B",
"gene_hgnc_id": 2183,
"hgvs_c": "n.2520A>T",
"hgvs_p": null,
"transcript": "ENST00000682145.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000682145.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 62,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS13B",
"gene_hgnc_id": 2183,
"hgvs_c": "n.2643A>T",
"hgvs_p": null,
"transcript": "ENST00000682153.1",
"protein_id": "ENSP00000507923.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000682153.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS13B",
"gene_hgnc_id": 2183,
"hgvs_c": "n.2643A>T",
"hgvs_p": null,
"transcript": "ENST00000682234.1",
"protein_id": "ENSP00000508225.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000682234.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 61,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS13B",
"gene_hgnc_id": 2183,
"hgvs_c": "n.2713A>T",
"hgvs_p": null,
"transcript": "ENST00000682358.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000682358.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 61,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS13B",
"gene_hgnc_id": 2183,
"hgvs_c": "n.2643A>T",
"hgvs_p": null,
"transcript": "ENST00000683334.1",
"protein_id": "ENSP00000507369.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000683334.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS13B",
"gene_hgnc_id": 2183,
"hgvs_c": "n.2709A>T",
"hgvs_p": null,
"transcript": "ENST00000683486.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000683486.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS13B",
"gene_hgnc_id": 2183,
"hgvs_c": "n.2815A>T",
"hgvs_p": null,
"transcript": "ENST00000683619.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000683619.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS13B",
"gene_hgnc_id": 2183,
"hgvs_c": "n.2724A>T",
"hgvs_p": null,
"transcript": "ENST00000683869.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000683869.1"
}
],
"gene_symbol": "VPS13B",
"gene_hgnc_id": 2183,
"dbsnp": "rs148777544",
"frequency_reference_population": 0.0004212874,
"hom_count_reference_population": 2,
"allele_count_reference_population": 680,
"gnomad_exomes_af": 0.000234637,
"gnomad_genomes_af": 0.00221317,
"gnomad_exomes_ac": 343,
"gnomad_genomes_ac": 337,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 2,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.011182785034179688,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.176,
"revel_prediction": "Benign",
"alphamissense_score": 0.8157,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.21,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 6.563,
"phylop100way_prediction": "Uncertain_significance",
"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": -13,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6,BS1,BS2",
"acmg_by_gene": [
{
"score": -13,
"benign_score": 13,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_017890.5",
"gene_symbol": "VPS13B",
"hgnc_id": 2183,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2643A>T",
"hgvs_p": "p.Lys881Asn"
}
],
"clinvar_disease": "Cohen syndrome,Inborn genetic diseases,VPS13B-related disorder,not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:2 LB:3 B:2",
"phenotype_combined": "not specified|Cohen syndrome|Inborn genetic diseases|VPS13B-related disorder|not provided",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}