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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: 9-98306266-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=98306266&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "9",
"pos": 98306266,
"ref": "C",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_005458.8",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GABBR2",
"gene_hgnc_id": 4507,
"hgvs_c": "c.2084G>T",
"hgvs_p": "p.Ser695Ile",
"transcript": "NM_005458.8",
"protein_id": "NP_005449.5",
"transcript_support_level": null,
"aa_start": 695,
"aa_end": null,
"aa_length": 941,
"cds_start": 2084,
"cds_end": null,
"cds_length": 2826,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000259455.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_005458.8"
},
{
"aa_ref": "S",
"aa_alt": "I",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GABBR2",
"gene_hgnc_id": 4507,
"hgvs_c": "c.2084G>T",
"hgvs_p": "p.Ser695Ile",
"transcript": "ENST00000259455.4",
"protein_id": "ENSP00000259455.2",
"transcript_support_level": 1,
"aa_start": 695,
"aa_end": null,
"aa_length": 941,
"cds_start": 2084,
"cds_end": null,
"cds_length": 2826,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_005458.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000259455.4"
},
{
"aa_ref": "S",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GABBR2",
"gene_hgnc_id": 4507,
"hgvs_c": "c.2018G>T",
"hgvs_p": "p.Ser673Ile",
"transcript": "ENST00000931526.1",
"protein_id": "ENSP00000601585.1",
"transcript_support_level": null,
"aa_start": 673,
"aa_end": null,
"aa_length": 919,
"cds_start": 2018,
"cds_end": null,
"cds_length": 2760,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000931526.1"
},
{
"aa_ref": "S",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GABBR2",
"gene_hgnc_id": 4507,
"hgvs_c": "c.2003G>T",
"hgvs_p": "p.Ser668Ile",
"transcript": "ENST00000947376.1",
"protein_id": "ENSP00000617435.1",
"transcript_support_level": null,
"aa_start": 668,
"aa_end": null,
"aa_length": 914,
"cds_start": 2003,
"cds_end": null,
"cds_length": 2745,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000947376.1"
},
{
"aa_ref": "S",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GABBR2",
"gene_hgnc_id": 4507,
"hgvs_c": "c.311G>T",
"hgvs_p": "p.Ser104Ile",
"transcript": "ENST00000634457.1",
"protein_id": "ENSP00000489352.1",
"transcript_support_level": 5,
"aa_start": 104,
"aa_end": null,
"aa_length": 182,
"cds_start": 311,
"cds_end": null,
"cds_length": 550,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000634457.1"
},
{
"aa_ref": "S",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GABBR2",
"gene_hgnc_id": 4507,
"hgvs_c": "c.1790G>T",
"hgvs_p": "p.Ser597Ile",
"transcript": "XM_017015331.3",
"protein_id": "XP_016870820.1",
"transcript_support_level": null,
"aa_start": 597,
"aa_end": null,
"aa_length": 843,
"cds_start": 1790,
"cds_end": null,
"cds_length": 2532,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017015331.3"
},
{
"aa_ref": "S",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GABBR2",
"gene_hgnc_id": 4507,
"hgvs_c": "c.1310G>T",
"hgvs_p": "p.Ser437Ile",
"transcript": "XM_005252316.6",
"protein_id": "XP_005252373.1",
"transcript_support_level": null,
"aa_start": 437,
"aa_end": null,
"aa_length": 683,
"cds_start": 1310,
"cds_end": null,
"cds_length": 2052,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005252316.6"
},
{
"aa_ref": "S",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GABBR2",
"gene_hgnc_id": 4507,
"hgvs_c": "c.1310G>T",
"hgvs_p": "p.Ser437Ile",
"transcript": "XM_017015332.3",
"protein_id": "XP_016870821.1",
"transcript_support_level": null,
"aa_start": 437,
"aa_end": null,
"aa_length": 683,
"cds_start": 1310,
"cds_end": null,
"cds_length": 2052,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017015332.3"
},
{
"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": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GABBR2",
"gene_hgnc_id": 4507,
"hgvs_c": "n.306G>T",
"hgvs_p": null,
"transcript": "ENST00000634354.1",
"protein_id": null,
"transcript_support_level": 5,
"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": "ENST00000634354.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GABBR2",
"gene_hgnc_id": 4507,
"hgvs_c": "n.579G>T",
"hgvs_p": null,
"transcript": "ENST00000635462.1",
"protein_id": null,
"transcript_support_level": 2,
"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": "ENST00000635462.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GABBR2",
"gene_hgnc_id": 4507,
"hgvs_c": "n.1862G>T",
"hgvs_p": null,
"transcript": "ENST00000637410.1",
"protein_id": null,
"transcript_support_level": 5,
"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": "ENST00000637410.1"
}
],
"gene_symbol": "GABBR2",
"gene_hgnc_id": 4507,
"dbsnp": "rs1554689319",
"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": 0.9705921411514282,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.97,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9968,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.4,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.727,
"phylop100way_prediction": "Pathogenic",
"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": 11,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM1,PM2,PM5,PP3_Strong,PP5",
"acmg_by_gene": [
{
"score": 11,
"benign_score": 0,
"pathogenic_score": 11,
"criteria": [
"PM1",
"PM2",
"PM5",
"PP3_Strong",
"PP5"
],
"verdict": "Pathogenic",
"transcript": "NM_005458.8",
"gene_symbol": "GABBR2",
"hgnc_id": 4507,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.2084G>T",
"hgvs_p": "p.Ser695Ile"
}
],
"clinvar_disease": " 59,Developmental and epileptic encephalopathy",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Developmental and epileptic encephalopathy, 59",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}