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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: 20-58444159-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=20&pos=58444159&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "20",
"pos": 58444159,
"ref": "G",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_004738.5",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VAPB",
"gene_hgnc_id": 12649,
"hgvs_c": "c.656G>T",
"hgvs_p": "p.Gly219Val",
"transcript": "NM_004738.5",
"protein_id": "NP_004729.1",
"transcript_support_level": null,
"aa_start": 219,
"aa_end": null,
"aa_length": 243,
"cds_start": 656,
"cds_end": null,
"cds_length": 732,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000475243.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_004738.5"
},
{
"aa_ref": "G",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VAPB",
"gene_hgnc_id": 12649,
"hgvs_c": "c.656G>T",
"hgvs_p": "p.Gly219Val",
"transcript": "ENST00000475243.6",
"protein_id": "ENSP00000417175.1",
"transcript_support_level": 1,
"aa_start": 219,
"aa_end": null,
"aa_length": 243,
"cds_start": 656,
"cds_end": null,
"cds_length": 732,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_004738.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000475243.6"
},
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VAPB",
"gene_hgnc_id": 12649,
"hgvs_c": "c.294G>T",
"hgvs_p": "p.Arg98Ser",
"transcript": "ENST00000395802.7",
"protein_id": "ENSP00000379147.3",
"transcript_support_level": 1,
"aa_start": 98,
"aa_end": null,
"aa_length": 99,
"cds_start": 294,
"cds_end": null,
"cds_length": 300,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000395802.7"
},
{
"aa_ref": "G",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VAPB",
"gene_hgnc_id": 12649,
"hgvs_c": "c.716G>T",
"hgvs_p": "p.Gly239Val",
"transcript": "ENST00000903510.1",
"protein_id": "ENSP00000573569.1",
"transcript_support_level": null,
"aa_start": 239,
"aa_end": null,
"aa_length": 263,
"cds_start": 716,
"cds_end": null,
"cds_length": 792,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000903510.1"
},
{
"aa_ref": "G",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VAPB",
"gene_hgnc_id": 12649,
"hgvs_c": "c.575G>T",
"hgvs_p": "p.Gly192Val",
"transcript": "ENST00000903509.1",
"protein_id": "ENSP00000573568.1",
"transcript_support_level": null,
"aa_start": 192,
"aa_end": null,
"aa_length": 216,
"cds_start": 575,
"cds_end": null,
"cds_length": 651,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000903509.1"
},
{
"aa_ref": "G",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VAPB",
"gene_hgnc_id": 12649,
"hgvs_c": "c.503G>T",
"hgvs_p": "p.Gly168Val",
"transcript": "ENST00000903508.1",
"protein_id": "ENSP00000573567.1",
"transcript_support_level": null,
"aa_start": 168,
"aa_end": null,
"aa_length": 192,
"cds_start": 503,
"cds_end": null,
"cds_length": 579,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000903508.1"
},
{
"aa_ref": "G",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VAPB",
"gene_hgnc_id": 12649,
"hgvs_c": "c.422G>T",
"hgvs_p": "p.Gly141Val",
"transcript": "ENST00000946349.1",
"protein_id": "ENSP00000616408.1",
"transcript_support_level": null,
"aa_start": 141,
"aa_end": null,
"aa_length": 165,
"cds_start": 422,
"cds_end": null,
"cds_length": 498,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000946349.1"
},
{
"aa_ref": "G",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VAPB",
"gene_hgnc_id": 12649,
"hgvs_c": "c.398G>T",
"hgvs_p": "p.Gly133Val",
"transcript": "ENST00000915806.1",
"protein_id": "ENSP00000585865.1",
"transcript_support_level": null,
"aa_start": 133,
"aa_end": null,
"aa_length": 157,
"cds_start": 398,
"cds_end": null,
"cds_length": 474,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000915806.1"
},
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VAPB",
"gene_hgnc_id": 12649,
"hgvs_c": "c.294G>T",
"hgvs_p": "p.Arg98Ser",
"transcript": "NM_001195677.2",
"protein_id": "NP_001182606.1",
"transcript_support_level": null,
"aa_start": 98,
"aa_end": null,
"aa_length": 99,
"cds_start": 294,
"cds_end": null,
"cds_length": 300,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001195677.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VAPB",
"gene_hgnc_id": 12649,
"hgvs_c": "n.850G>T",
"hgvs_p": null,
"transcript": "ENST00000265619.6",
"protein_id": null,
"transcript_support_level": 2,
"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": "ENST00000265619.6"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VAPB",
"gene_hgnc_id": 12649,
"hgvs_c": "n.1000G>T",
"hgvs_p": null,
"transcript": "ENST00000463370.5",
"protein_id": null,
"transcript_support_level": 2,
"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": "ENST00000463370.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"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": "VAPB",
"gene_hgnc_id": 12649,
"hgvs_c": "n.2190G>T",
"hgvs_p": null,
"transcript": "ENST00000476395.1",
"protein_id": null,
"transcript_support_level": 2,
"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": "ENST00000476395.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VAPB",
"gene_hgnc_id": 12649,
"hgvs_c": "n.*255G>T",
"hgvs_p": null,
"transcript": "ENST00000520497.1",
"protein_id": "ENSP00000430426.1",
"transcript_support_level": 2,
"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": "ENST00000520497.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VAPB",
"gene_hgnc_id": 12649,
"hgvs_c": "n.702G>T",
"hgvs_p": null,
"transcript": "NR_036633.2",
"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": "NR_036633.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VAPB",
"gene_hgnc_id": 12649,
"hgvs_c": "n.*255G>T",
"hgvs_p": null,
"transcript": "ENST00000520497.1",
"protein_id": "ENSP00000430426.1",
"transcript_support_level": 2,
"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": "ENST00000520497.1"
}
],
"gene_symbol": "VAPB",
"gene_hgnc_id": 12649,
"dbsnp": "rs786205553",
"frequency_reference_population": 0.00001162875,
"hom_count_reference_population": 0,
"allele_count_reference_population": 17,
"gnomad_exomes_af": 0.0000116288,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 17,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.6999962329864502,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.421,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.0946,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": 0.27,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 9.024,
"phylop100way_prediction": "Pathogenic",
"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": -4,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BS2",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BS2"
],
"verdict": "Likely_benign",
"transcript": "NM_004738.5",
"gene_symbol": "VAPB",
"hgnc_id": 12649,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.656G>T",
"hgvs_p": "p.Gly219Val"
}
],
"clinvar_disease": " autosomal dominant,Adult-onset proximal spinal muscular atrophy,Amyotrophic lateral sclerosis type 8,not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:4 LB:1",
"phenotype_combined": "not specified|not provided|Amyotrophic lateral sclerosis type 8;Adult-onset proximal spinal muscular atrophy, autosomal dominant",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}