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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: 9-109141519-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=109141519&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 7,
"criteria": [
"BP4_Moderate",
"BP6",
"BS2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "FRRS1L",
"hgnc_id": 1362,
"hgvs_c": "c.533T>C",
"hgvs_p": "p.Val178Ala",
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -7,
"transcript": "NM_014334.4",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Moderate,BP6,BS2",
"acmg_score": -7,
"allele_count_reference_population": 1707,
"alphamissense_prediction": "Pathogenic",
"alphamissense_score": 0.8599,
"alt": "G",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Uncertain_significance",
"bayesdelnoaf_score": 0.09,
"chr": "9",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_disease": " 37,Developmental and epileptic encephalopathy,not provided",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:2 LB:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.2591945230960846,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 293,
"aa_ref": "V",
"aa_start": 178,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8155,
"cdna_start": 644,
"cds_end": null,
"cds_length": 882,
"cds_start": 533,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "NM_014334.4",
"gene_hgnc_id": 1362,
"gene_symbol": "FRRS1L",
"hgvs_c": "c.533T>C",
"hgvs_p": "p.Val178Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000561981.5",
"protein_coding": true,
"protein_id": "NP_055149.3",
"strand": false,
"transcript": "NM_014334.4",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 293,
"aa_ref": "V",
"aa_start": 178,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 8155,
"cdna_start": 644,
"cds_end": null,
"cds_length": 882,
"cds_start": 533,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000561981.5",
"gene_hgnc_id": 1362,
"gene_symbol": "FRRS1L",
"hgvs_c": "c.533T>C",
"hgvs_p": "p.Val178Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_014334.4",
"protein_coding": true,
"protein_id": "ENSP00000477141.2",
"strand": false,
"transcript": "ENST00000561981.5",
"transcript_support_level": 1
},
{
"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": 3497,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000642157.1",
"gene_hgnc_id": 1362,
"gene_symbol": "FRRS1L",
"hgvs_c": "n.2768T>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000642157.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 711,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 6,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000644736.1",
"gene_hgnc_id": 1362,
"gene_symbol": "FRRS1L",
"hgvs_c": "n.*505T>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000494579.1",
"strand": false,
"transcript": "ENST00000644736.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 671,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 4,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000644747.1",
"gene_hgnc_id": 1362,
"gene_symbol": "FRRS1L",
"hgvs_c": "n.*151T>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000493964.1",
"strand": false,
"transcript": "ENST00000644747.1",
"transcript_support_level": null
},
{
"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": 5146,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000645180.1",
"gene_hgnc_id": 1362,
"gene_symbol": "FRRS1L",
"hgvs_c": "n.1284T>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000645180.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 711,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 6,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000644736.1",
"gene_hgnc_id": 1362,
"gene_symbol": "FRRS1L",
"hgvs_c": "n.*505T>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000494579.1",
"strand": false,
"transcript": "ENST00000644736.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 671,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 4,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000644747.1",
"gene_hgnc_id": 1362,
"gene_symbol": "FRRS1L",
"hgvs_c": "n.*151T>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000493964.1",
"strand": false,
"transcript": "ENST00000644747.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 445,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000642299.1",
"gene_hgnc_id": 1362,
"gene_symbol": "FRRS1L",
"hgvs_c": "n.*380T>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000495137.1",
"strand": true,
"transcript": "ENST00000642299.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs148986846",
"effect": "missense_variant",
"frequency_reference_population": 0.0010575344,
"gene_hgnc_id": 1362,
"gene_symbol": "FRRS1L",
"gnomad_exomes_ac": 1634,
"gnomad_exomes_af": 0.00111775,
"gnomad_exomes_homalt": 3,
"gnomad_genomes_ac": 73,
"gnomad_genomes_af": 0.000479437,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 3,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"phenotype_combined": "Developmental and epileptic encephalopathy, 37|not provided",
"phylop100way_prediction": "Pathogenic",
"phylop100way_score": 9.325,
"pos": 109141519,
"ref": "A",
"revel_prediction": "Uncertain_significance",
"revel_score": 0.432,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_014334.4"
}
]
}