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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: 15-22812252-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=15&pos=22812252&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PS3",
"PM2",
"PP3",
"PP5_Very_Strong"
],
"effects": [
"missense_variant",
"splice_region_variant"
],
"gene_symbol": "NIPA1",
"hgnc_id": 17043,
"hgvs_c": "c.316G>A",
"hgvs_p": "p.Gly106Arg",
"inheritance_mode": "AD",
"pathogenic_score": 15,
"score": 15,
"transcript": "NM_144599.5",
"verdict": "Pathogenic"
}
],
"acmg_classification": "Pathogenic",
"acmg_criteria": "PS3,PM2,PP3,PP5_Very_Strong",
"acmg_score": 15,
"allele_count_reference_population": 0,
"alphamissense_prediction": null,
"alphamissense_score": 0.9849,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.57,
"chr": "15",
"clinvar_classification": "Pathogenic",
"clinvar_disease": "Hereditary spastic paraplegia,Hereditary spastic paraplegia 6,Spastic paraplegia,not provided",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:12",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.8561775088310242,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 329,
"aa_ref": "G",
"aa_start": 106,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6553,
"cdna_start": 329,
"cds_end": null,
"cds_length": 990,
"cds_start": 316,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 5,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "NM_144599.5",
"gene_hgnc_id": 17043,
"gene_symbol": "NIPA1",
"hgvs_c": "c.316G>A",
"hgvs_p": "p.Gly106Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000337435.9",
"protein_coding": true,
"protein_id": "NP_653200.2",
"strand": true,
"transcript": "NM_144599.5",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 329,
"aa_ref": "G",
"aa_start": 106,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 6553,
"cdna_start": 329,
"cds_end": null,
"cds_length": 990,
"cds_start": 316,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 5,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000337435.9",
"gene_hgnc_id": 17043,
"gene_symbol": "NIPA1",
"hgvs_c": "c.316G>A",
"hgvs_p": "p.Gly106Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_144599.5",
"protein_coding": true,
"protein_id": "ENSP00000337452.4",
"strand": true,
"transcript": "ENST00000337435.9",
"transcript_support_level": 1
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 254,
"aa_ref": "G",
"aa_start": 31,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7613,
"cdna_start": 1389,
"cds_end": null,
"cds_length": 765,
"cds_start": 91,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 5,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000437912.6",
"gene_hgnc_id": 17043,
"gene_symbol": "NIPA1",
"hgvs_c": "c.91G>A",
"hgvs_p": "p.Gly31Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000393962.2",
"strand": true,
"transcript": "ENST00000437912.6",
"transcript_support_level": 1
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 254,
"aa_ref": "G",
"aa_start": 31,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1675,
"cdna_start": 488,
"cds_end": null,
"cds_length": 765,
"cds_start": 91,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 5,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000561183.5",
"gene_hgnc_id": 17043,
"gene_symbol": "NIPA1",
"hgvs_c": "c.91G>A",
"hgvs_p": "p.Gly31Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000453722.1",
"strand": true,
"transcript": "ENST00000561183.5",
"transcript_support_level": 1
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 254,
"aa_ref": "G",
"aa_start": 31,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6386,
"cdna_start": 162,
"cds_end": null,
"cds_length": 765,
"cds_start": 91,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 5,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "NM_001142275.1",
"gene_hgnc_id": 17043,
"gene_symbol": "NIPA1",
"hgvs_c": "c.91G>A",
"hgvs_p": "p.Gly31Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001135747.1",
"strand": true,
"transcript": "NM_001142275.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 245,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1324,
"cdna_start": null,
"cds_end": null,
"cds_length": 738,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000905597.1",
"gene_hgnc_id": 17043,
"gene_symbol": "NIPA1",
"hgvs_c": "c.226+1456G>A",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000575656.1",
"strand": true,
"transcript": "ENST00000905597.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 229,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1927,
"cdna_start": null,
"cds_end": null,
"cds_length": 690,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000941787.1",
"gene_hgnc_id": 17043,
"gene_symbol": "NIPA1",
"hgvs_c": "c.179-11476G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000611846.1",
"strand": true,
"transcript": "ENST00000941787.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 582,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_count": 6,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000557930.1",
"gene_hgnc_id": 17043,
"gene_symbol": "NIPA1",
"hgvs_c": "n.160G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000453797.1",
"strand": true,
"transcript": "ENST00000557930.1",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 2799,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_count": 6,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000559448.5",
"gene_hgnc_id": 17043,
"gene_symbol": "NIPA1",
"hgvs_c": "n.205G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000453286.1",
"strand": true,
"transcript": "ENST00000559448.5",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 575,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_count": 7,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000560069.5",
"gene_hgnc_id": 17043,
"gene_symbol": "NIPA1",
"hgvs_c": "n.169G>A",
"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": "ENST00000560069.5",
"transcript_support_level": 4
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": "Pathogenic",
"dbscsnv_ada_score": 0.992782413906273,
"dbsnp": "rs104894490",
"effect": "missense_variant,splice_region_variant",
"frequency_reference_population": null,
"gene_hgnc_id": 17043,
"gene_symbol": "NIPA1",
"gnomad_exomes_ac": 0,
"gnomad_exomes_af": 0,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Pathogenic",
"phenotype_combined": "Hereditary spastic paraplegia 6|Hereditary spastic paraplegia|not provided|Spastic paraplegia",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 7.419,
"pos": 22812252,
"ref": "G",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Pathogenic",
"splice_score_selected": 0.9259999990463257,
"splice_source_selected": "dbscSNV1_RF",
"spliceai_max_prediction": "Pathogenic",
"spliceai_max_score": 0.95,
"transcript": "NM_144599.5"
}
]
}