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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: 8-24956452-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=8&pos=24956452&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "8",
"pos": 24956452,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_006158.5",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEFL",
"gene_hgnc_id": 7739,
"hgvs_c": "c.64C>T",
"hgvs_p": "p.Pro22Ser",
"transcript": "NM_006158.5",
"protein_id": "NP_006149.2",
"transcript_support_level": null,
"aa_start": 22,
"aa_end": null,
"aa_length": 543,
"cds_start": 64,
"cds_end": null,
"cds_length": 1632,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000610854.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_006158.5"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEFL",
"gene_hgnc_id": 7739,
"hgvs_c": "c.64C>T",
"hgvs_p": "p.Pro22Ser",
"transcript": "ENST00000610854.2",
"protein_id": "ENSP00000482169.2",
"transcript_support_level": 1,
"aa_start": 22,
"aa_end": null,
"aa_length": 543,
"cds_start": 64,
"cds_end": null,
"cds_length": 1632,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_006158.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000610854.2"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEFL",
"gene_hgnc_id": 7739,
"hgvs_c": "c.64C>T",
"hgvs_p": "p.Pro22Ser",
"transcript": "ENST00000916556.1",
"protein_id": "ENSP00000586615.1",
"transcript_support_level": null,
"aa_start": 22,
"aa_end": null,
"aa_length": 539,
"cds_start": 64,
"cds_end": null,
"cds_length": 1620,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000916556.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000272157",
"gene_hgnc_id": null,
"hgvs_c": "n.762G>A",
"hgvs_p": null,
"transcript": "ENST00000607735.3",
"protein_id": null,
"transcript_support_level": 6,
"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": "ENST00000607735.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEFL",
"gene_hgnc_id": 7739,
"hgvs_c": "n.270C>T",
"hgvs_p": null,
"transcript": "ENST00000615973.1",
"protein_id": null,
"transcript_support_level": 6,
"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": "ENST00000615973.1"
}
],
"gene_symbol": "NEFL",
"gene_hgnc_id": 7739,
"dbsnp": "rs28928910",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.28821253776550293,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": 0.1492,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.21,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.905,
"phylop100way_prediction": "Benign",
"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": 18,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PS3,PM1,PM2,PM5,PP2,PP5_Very_Strong,BP4",
"acmg_by_gene": [
{
"score": 18,
"benign_score": 1,
"pathogenic_score": 19,
"criteria": [
"PS3",
"PM1",
"PM2",
"PM5",
"PP2",
"PP5_Very_Strong",
"BP4"
],
"verdict": "Pathogenic",
"transcript": "NM_006158.5",
"gene_symbol": "NEFL",
"hgnc_id": 7739,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.64C>T",
"hgvs_p": "p.Pro22Ser"
},
{
"score": 13,
"benign_score": 1,
"pathogenic_score": 14,
"criteria": [
"PS3",
"PM2",
"PP5_Very_Strong",
"BP4"
],
"verdict": "Pathogenic",
"transcript": "ENST00000607735.3",
"gene_symbol": "ENSG00000272157",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.762G>A",
"hgvs_p": null
}
],
"clinvar_disease": "Charcot-Marie-Tooth disease type 1C,Charcot-Marie-Tooth disease type 1F,Charcot-Marie-Tooth disease type 2E,Decreased nerve conduction velocity,Distal lower limb muscle weakness,Distal muscle weakness,Hand muscle atrophy,Inborn genetic diseases,Peripheral demyelination,Peripheral neuropathy,Pes cavus,not provided",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:5 LP:1 O:2",
"phenotype_combined": "Charcot-Marie-Tooth disease type 2E|Charcot-Marie-Tooth disease type 1F|not provided|Peripheral neuropathy;Distal muscle weakness;Peripheral demyelination;Hand muscle atrophy;Decreased nerve conduction velocity|Charcot-Marie-Tooth disease type 1C|Peripheral neuropathy;Pes cavus;Distal lower limb muscle weakness|Inborn genetic diseases",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}