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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: 6-31860563-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=31860563&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "6",
"pos": 31860563,
"ref": "C",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000375631.5",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEU1",
"gene_hgnc_id": 7758,
"hgvs_c": "c.674G>C",
"hgvs_p": "p.Arg225Pro",
"transcript": "NM_000434.4",
"protein_id": "NP_000425.1",
"transcript_support_level": null,
"aa_start": 225,
"aa_end": null,
"aa_length": 415,
"cds_start": 674,
"cds_end": null,
"cds_length": 1248,
"cdna_start": 719,
"cdna_end": null,
"cdna_length": 3353,
"mane_select": "ENST00000375631.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "P",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEU1",
"gene_hgnc_id": 7758,
"hgvs_c": "c.674G>C",
"hgvs_p": "p.Arg225Pro",
"transcript": "ENST00000375631.5",
"protein_id": "ENSP00000364782.4",
"transcript_support_level": 1,
"aa_start": 225,
"aa_end": null,
"aa_length": 415,
"cds_start": 674,
"cds_end": null,
"cds_length": 1248,
"cdna_start": 719,
"cdna_end": null,
"cdna_length": 3353,
"mane_select": "NM_000434.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEU1",
"gene_hgnc_id": 7758,
"hgvs_c": "c.668G>C",
"hgvs_p": "p.Arg223Pro",
"transcript": "ENST00000850553.1",
"protein_id": "ENSP00000520846.1",
"transcript_support_level": null,
"aa_start": 223,
"aa_end": null,
"aa_length": 413,
"cds_start": 668,
"cds_end": null,
"cds_length": 1242,
"cdna_start": 712,
"cdna_end": null,
"cdna_length": 3942,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"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": "NEU1",
"gene_hgnc_id": 7758,
"hgvs_c": "n.703G>C",
"hgvs_p": null,
"transcript": "ENST00000480384.1",
"protein_id": null,
"transcript_support_level": 2,
"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": 2214,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEU1",
"gene_hgnc_id": 7758,
"hgvs_c": "n.674G>C",
"hgvs_p": null,
"transcript": "ENST00000491768.5",
"protein_id": "ENSP00000433127.1",
"transcript_support_level": 5,
"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": 1875,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEU1",
"gene_hgnc_id": 7758,
"hgvs_c": "n.1808G>C",
"hgvs_p": null,
"transcript": "ENST00000495807.1",
"protein_id": null,
"transcript_support_level": 2,
"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": 4616,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEU1",
"gene_hgnc_id": 7758,
"hgvs_c": "n.1917G>C",
"hgvs_p": null,
"transcript": "ENST00000677054.1",
"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": 3047,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEU1",
"gene_hgnc_id": 7758,
"hgvs_c": "n.782G>C",
"hgvs_p": null,
"transcript": "ENST00000677512.1",
"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": 1973,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEU1",
"gene_hgnc_id": 7758,
"hgvs_c": "n.1348G>C",
"hgvs_p": null,
"transcript": "ENST00000678869.1",
"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": 2338,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEU1",
"gene_hgnc_id": 7758,
"hgvs_c": "n.411G>C",
"hgvs_p": null,
"transcript": "ENST00000850554.1",
"protein_id": "ENSP00000520847.1",
"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": 1549,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEU1",
"gene_hgnc_id": 7758,
"hgvs_c": "n.427G>C",
"hgvs_p": null,
"transcript": "ENST00000850555.1",
"protein_id": "ENSP00000520848.1",
"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": 1572,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "NEU1",
"gene_hgnc_id": 7758,
"dbsnp": "rs104893980",
"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": 0.9478390216827393,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.07999999821186066,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.618,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.6721,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.24,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 2.19,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.08,
"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": 10,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM1,PM2,PP2,PP3_Strong,PP5",
"acmg_by_gene": [
{
"score": 10,
"benign_score": 0,
"pathogenic_score": 10,
"criteria": [
"PM1",
"PM2",
"PP2",
"PP3_Strong",
"PP5"
],
"verdict": "Pathogenic",
"transcript": "ENST00000375631.5",
"gene_symbol": "NEU1",
"hgnc_id": 7758,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.674G>C",
"hgvs_p": "p.Arg225Pro"
}
],
"clinvar_disease": "Sialidosis type 2",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Sialidosis type 2",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}