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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: 12-57582629-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=57582629&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 57582629,
"ref": "G",
"alt": "A",
"effect": "missense_variant,splice_region_variant",
"transcript": "ENST00000455537.7",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KIF5A",
"gene_hgnc_id": 6323,
"hgvs_c": "c.3020G>A",
"hgvs_p": "p.Arg1007Lys",
"transcript": "NM_004984.4",
"protein_id": "NP_004975.2",
"transcript_support_level": null,
"aa_start": 1007,
"aa_end": null,
"aa_length": 1032,
"cds_start": 3020,
"cds_end": null,
"cds_length": 3099,
"cdna_start": 3248,
"cdna_end": null,
"cdna_length": 5779,
"mane_select": "ENST00000455537.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "K",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KIF5A",
"gene_hgnc_id": 6323,
"hgvs_c": "c.3020G>A",
"hgvs_p": "p.Arg1007Lys",
"transcript": "ENST00000455537.7",
"protein_id": "ENSP00000408979.2",
"transcript_support_level": 1,
"aa_start": 1007,
"aa_end": null,
"aa_length": 1032,
"cds_start": 3020,
"cds_end": null,
"cds_length": 3099,
"cdna_start": 3248,
"cdna_end": null,
"cdna_length": 5779,
"mane_select": "NM_004984.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KIF5A",
"gene_hgnc_id": 6323,
"hgvs_c": "c.3041G>A",
"hgvs_p": "p.Arg1014Lys",
"transcript": "ENST00000674619.1",
"protein_id": "ENSP00000502270.1",
"transcript_support_level": null,
"aa_start": 1014,
"aa_end": null,
"aa_length": 1039,
"cds_start": 3041,
"cds_end": null,
"cds_length": 3120,
"cdna_start": 3286,
"cdna_end": null,
"cdna_length": 5814,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KIF5A",
"gene_hgnc_id": 6323,
"hgvs_c": "c.44G>A",
"hgvs_p": "p.Arg15Lys",
"transcript": "ENST00000676437.1",
"protein_id": "ENSP00000502358.1",
"transcript_support_level": null,
"aa_start": 15,
"aa_end": null,
"aa_length": 113,
"cds_start": 44,
"cds_end": null,
"cds_length": 342,
"cdna_start": 45,
"cdna_end": null,
"cdna_length": 3314,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KIF5A",
"gene_hgnc_id": 6323,
"hgvs_c": "c.2915G>A",
"hgvs_p": "p.Arg972Lys",
"transcript": "ENST00000676457.1",
"protein_id": "ENSP00000501588.1",
"transcript_support_level": null,
"aa_start": 972,
"aa_end": null,
"aa_length": 997,
"cds_start": 2915,
"cds_end": null,
"cds_length": 2994,
"cdna_start": 3082,
"cdna_end": null,
"cdna_length": 5572,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KIF5A",
"gene_hgnc_id": 6323,
"hgvs_c": "c.2753G>A",
"hgvs_p": "p.Arg918Lys",
"transcript": "NM_001354705.2",
"protein_id": "NP_001341634.1",
"transcript_support_level": null,
"aa_start": 918,
"aa_end": null,
"aa_length": 943,
"cds_start": 2753,
"cds_end": null,
"cds_length": 2832,
"cdna_start": 2981,
"cdna_end": null,
"cdna_length": 5512,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KIF5A",
"gene_hgnc_id": 6323,
"hgvs_c": "c.2753G>A",
"hgvs_p": "p.Arg918Lys",
"transcript": "ENST00000286452.5",
"protein_id": "ENSP00000286452.5",
"transcript_support_level": 2,
"aa_start": 918,
"aa_end": null,
"aa_length": 943,
"cds_start": 2753,
"cds_end": null,
"cds_length": 2832,
"cdna_start": 2981,
"cdna_end": null,
"cdna_length": 3527,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KIF5A",
"gene_hgnc_id": 6323,
"hgvs_c": "c.26G>A",
"hgvs_p": "p.Ser9Asn",
"transcript": "ENST00000675866.1",
"protein_id": "ENSP00000502341.1",
"transcript_support_level": null,
"aa_start": 9,
"aa_end": null,
"aa_length": 10,
"cds_start": 26,
"cds_end": null,
"cds_length": 33,
"cdna_start": 28,
"cdna_end": null,
"cdna_length": 459,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "?",
"aa_alt": "?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KIF5A",
"gene_hgnc_id": 6323,
"hgvs_c": "c.98G>A",
"hgvs_p": "p.???33???",
"transcript": "ENST00000676055.1",
"protein_id": "ENSP00000501739.1",
"transcript_support_level": null,
"aa_start": 33,
"aa_end": null,
"aa_length": 31,
"cds_start": 98,
"cds_end": null,
"cds_length": 98,
"cdna_start": 99,
"cdna_end": null,
"cdna_length": 99,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": "KIF5A",
"gene_hgnc_id": 6323,
"hgvs_c": "n.303G>A",
"hgvs_p": null,
"transcript": "ENST00000552227.1",
"protein_id": null,
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 548,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KIF5A",
"gene_hgnc_id": 6323,
"hgvs_c": "n.28G>A",
"hgvs_p": null,
"transcript": "ENST00000675201.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 150,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KIF5A",
"gene_hgnc_id": 6323,
"hgvs_c": "n.1073G>A",
"hgvs_p": null,
"transcript": "ENST00000675737.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3298,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KIF5A",
"gene_hgnc_id": 6323,
"hgvs_c": "n.2543G>A",
"hgvs_p": null,
"transcript": "ENST00000675882.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5336,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KIF5A",
"gene_hgnc_id": 6323,
"hgvs_c": "n.1578G>A",
"hgvs_p": null,
"transcript": "ENST00000675929.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3286,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KIF5A",
"gene_hgnc_id": 6323,
"hgvs_c": "n.28G>A",
"hgvs_p": null,
"transcript": "ENST00000676265.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 228,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "KIF5A",
"gene_hgnc_id": 6323,
"hgvs_c": "c.83-472G>A",
"hgvs_p": null,
"transcript": "ENST00000675697.1",
"protein_id": "ENSP00000501809.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 67,
"cds_start": -4,
"cds_end": null,
"cds_length": 204,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 629,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "KIF5A",
"gene_hgnc_id": 6323,
"dbsnp": "rs1060502523",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": 0,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 0,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.2299477458000183,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 1,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": 0.31,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.2544,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.12,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 8.237,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.66,
"spliceai_max_prediction": "Pathogenic",
"dbscsnv_ada_score": 0.999994233162681,
"dbscsnv_ada_prediction": "Pathogenic",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 16,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM2,PM5,PP3_Strong,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 16,
"benign_score": 0,
"pathogenic_score": 16,
"criteria": [
"PM2",
"PM5",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000455537.7",
"gene_symbol": "KIF5A",
"hgnc_id": 6323,
"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.3020G>A",
"hgvs_p": "p.Arg1007Lys"
}
],
"clinvar_disease": "Spastic paraplegia,not provided",
"clinvar_classification": "Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LP:2",
"phenotype_combined": "Spastic paraplegia|not provided",
"pathogenicity_classification_combined": "Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}