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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: 12-57569275-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=57569275&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM1",
"PM2",
"PM5",
"PP3_Strong",
"PP5_Very_Strong"
],
"effects": [
"missense_variant"
],
"gene_symbol": "KIF5A",
"hgnc_id": 6323,
"hgvs_c": "c.839G>A",
"hgvs_p": "p.Arg280His",
"inheritance_mode": "AD",
"pathogenic_score": 18,
"score": 18,
"transcript": "NM_004984.4",
"verdict": "Pathogenic"
}
],
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM1,PM2,PM5,PP3_Strong,PP5_Very_Strong",
"acmg_score": 18,
"allele_count_reference_population": 1,
"alphamissense_prediction": null,
"alphamissense_score": 0.9987,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.44,
"chr": "12",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_disease": "Demyelinating peripheral neuropathy,Hereditary spastic paraplegia,Hereditary spastic paraplegia 10,Spastic paraplegia,not provided",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:8 LP:1",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.9751688241958618,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 1032,
"aa_ref": "R",
"aa_start": 280,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5779,
"cdna_start": 1067,
"cds_end": null,
"cds_length": 3099,
"cds_start": 839,
"consequences": [
"missense_variant"
],
"exon_count": 29,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "NM_004984.4",
"gene_hgnc_id": 6323,
"gene_symbol": "KIF5A",
"hgvs_c": "c.839G>A",
"hgvs_p": "p.Arg280His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000455537.7",
"protein_coding": true,
"protein_id": "NP_004975.2",
"strand": true,
"transcript": "NM_004984.4",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 1032,
"aa_ref": "R",
"aa_start": 280,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 5779,
"cdna_start": 1067,
"cds_end": null,
"cds_length": 3099,
"cds_start": 839,
"consequences": [
"missense_variant"
],
"exon_count": 29,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000455537.7",
"gene_hgnc_id": 6323,
"gene_symbol": "KIF5A",
"hgvs_c": "c.839G>A",
"hgvs_p": "p.Arg280His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_004984.4",
"protein_coding": true,
"protein_id": "ENSP00000408979.2",
"strand": true,
"transcript": "ENST00000455537.7",
"transcript_support_level": 1
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 1039,
"aa_ref": "R",
"aa_start": 280,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5814,
"cdna_start": 1084,
"cds_end": null,
"cds_length": 3120,
"cds_start": 839,
"consequences": [
"missense_variant"
],
"exon_count": 30,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000674619.1",
"gene_hgnc_id": 6323,
"gene_symbol": "KIF5A",
"hgvs_c": "c.839G>A",
"hgvs_p": "p.Arg280His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000502270.1",
"strand": true,
"transcript": "ENST00000674619.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 1032,
"aa_ref": "R",
"aa_start": 280,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6790,
"cdna_start": 1081,
"cds_end": null,
"cds_length": 3099,
"cds_start": 839,
"consequences": [
"missense_variant"
],
"exon_count": 28,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000938849.1",
"gene_hgnc_id": 6323,
"gene_symbol": "KIF5A",
"hgvs_c": "c.839G>A",
"hgvs_p": "p.Arg280His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000608908.1",
"strand": true,
"transcript": "ENST00000938849.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 1031,
"aa_ref": "R",
"aa_start": 280,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5795,
"cdna_start": 1097,
"cds_end": null,
"cds_length": 3096,
"cds_start": 839,
"consequences": [
"missense_variant"
],
"exon_count": 29,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000910206.1",
"gene_hgnc_id": 6323,
"gene_symbol": "KIF5A",
"hgvs_c": "c.839G>A",
"hgvs_p": "p.Arg280His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000580265.1",
"strand": true,
"transcript": "ENST00000910206.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 1031,
"aa_ref": "R",
"aa_start": 280,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5773,
"cdna_start": 1066,
"cds_end": null,
"cds_length": 3096,
"cds_start": 839,
"consequences": [
"missense_variant"
],
"exon_count": 29,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000910207.1",
"gene_hgnc_id": 6323,
"gene_symbol": "KIF5A",
"hgvs_c": "c.839G>A",
"hgvs_p": "p.Arg280His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000580266.1",
"strand": true,
"transcript": "ENST00000910207.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 997,
"aa_ref": "R",
"aa_start": 245,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5572,
"cdna_start": 901,
"cds_end": null,
"cds_length": 2994,
"cds_start": 734,
"consequences": [
"missense_variant"
],
"exon_count": 28,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000676457.1",
"gene_hgnc_id": 6323,
"gene_symbol": "KIF5A",
"hgvs_c": "c.734G>A",
"hgvs_p": "p.Arg245His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000501588.1",
"strand": true,
"transcript": "ENST00000676457.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 943,
"aa_ref": "R",
"aa_start": 191,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5512,
"cdna_start": 800,
"cds_end": null,
"cds_length": 2832,
"cds_start": 572,
"consequences": [
"missense_variant"
],
"exon_count": 26,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "NM_001354705.2",
"gene_hgnc_id": 6323,
"gene_symbol": "KIF5A",
"hgvs_c": "c.572G>A",
"hgvs_p": "p.Arg191His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001341634.1",
"strand": true,
"transcript": "NM_001354705.2",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 943,
"aa_ref": "R",
"aa_start": 191,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3527,
"cdna_start": 800,
"cds_end": null,
"cds_length": 2832,
"cds_start": 572,
"consequences": [
"missense_variant"
],
"exon_count": 26,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000286452.5",
"gene_hgnc_id": 6323,
"gene_symbol": "KIF5A",
"hgvs_c": "c.572G>A",
"hgvs_p": "p.Arg191His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000286452.5",
"strand": true,
"transcript": "ENST00000286452.5",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 3726,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 12,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000676081.1",
"gene_hgnc_id": 6323,
"gene_symbol": "KIF5A",
"hgvs_c": "n.-16G>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": "ENST00000676081.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs387907288",
"effect": "missense_variant",
"frequency_reference_population": 6.840703e-7,
"gene_hgnc_id": 6323,
"gene_symbol": "KIF5A",
"gnomad_exomes_ac": 1,
"gnomad_exomes_af": 6.8407e-7,
"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/Likely pathogenic",
"phenotype_combined": "Hereditary spastic paraplegia 10|Hereditary spastic paraplegia|Spastic paraplegia|not provided|Demyelinating peripheral neuropathy",
"phylop100way_prediction": "Pathogenic",
"phylop100way_score": 9.864,
"pos": 57569275,
"ref": "G",
"revel_prediction": "Pathogenic",
"revel_score": 0.936,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.07000000029802322,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.07,
"transcript": "NM_004984.4"
}
]
}