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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: 19-35030822-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=35030822&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 35030822,
"ref": "T",
"alt": "C",
"effect": "start_lost",
"transcript": "NM_199037.5",
"consequences": [
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"start_lost"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN1B",
"gene_hgnc_id": 10586,
"hgvs_c": "c.2T>C",
"hgvs_p": "p.Met1?",
"transcript": "NM_001037.5",
"protein_id": "NP_001028.1",
"transcript_support_level": null,
"aa_start": 1,
"aa_end": null,
"aa_length": 218,
"cds_start": 2,
"cds_end": null,
"cds_length": 657,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000262631.11",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001037.5"
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"start_lost"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN1B",
"gene_hgnc_id": 10586,
"hgvs_c": "c.2T>C",
"hgvs_p": "p.Met1?",
"transcript": "ENST00000262631.11",
"protein_id": "ENSP00000262631.3",
"transcript_support_level": 1,
"aa_start": 1,
"aa_end": null,
"aa_length": 218,
"cds_start": 2,
"cds_end": null,
"cds_length": 657,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001037.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000262631.11"
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"start_lost"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN1B",
"gene_hgnc_id": 10586,
"hgvs_c": "c.2T>C",
"hgvs_p": "p.Met1?",
"transcript": "ENST00000415950.5",
"protein_id": "ENSP00000396915.2",
"transcript_support_level": 1,
"aa_start": 1,
"aa_end": null,
"aa_length": 268,
"cds_start": 2,
"cds_end": null,
"cds_length": 807,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000415950.5"
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"start_lost"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN1B",
"gene_hgnc_id": 10586,
"hgvs_c": "c.2T>C",
"hgvs_p": "p.Met1?",
"transcript": "ENST00000638536.1",
"protein_id": "ENSP00000492022.1",
"transcript_support_level": 1,
"aa_start": 1,
"aa_end": null,
"aa_length": 218,
"cds_start": 2,
"cds_end": null,
"cds_length": 657,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000638536.1"
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"start_lost"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN1B",
"gene_hgnc_id": 10586,
"hgvs_c": "c.2T>C",
"hgvs_p": "p.Met1?",
"transcript": "NM_199037.5",
"protein_id": "NP_950238.1",
"transcript_support_level": null,
"aa_start": 1,
"aa_end": null,
"aa_length": 268,
"cds_start": 2,
"cds_end": null,
"cds_length": 807,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_199037.5"
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"start_lost"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN1B",
"gene_hgnc_id": 10586,
"hgvs_c": "c.2T>C",
"hgvs_p": "p.Met1?",
"transcript": "ENST00000955983.1",
"protein_id": "ENSP00000626042.1",
"transcript_support_level": null,
"aa_start": 1,
"aa_end": null,
"aa_length": 191,
"cds_start": 2,
"cds_end": null,
"cds_length": 576,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000955983.1"
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"start_lost"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN1B",
"gene_hgnc_id": 10586,
"hgvs_c": "c.2T>C",
"hgvs_p": "p.Met1?",
"transcript": "ENST00000595652.5",
"protein_id": "ENSP00000468848.1",
"transcript_support_level": 2,
"aa_start": 1,
"aa_end": null,
"aa_length": 147,
"cds_start": 2,
"cds_end": null,
"cds_length": 444,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000595652.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "HPN-AS1",
"gene_hgnc_id": 47041,
"hgvs_c": "n.413-2264A>G",
"hgvs_p": null,
"transcript": "ENST00000796454.1",
"protein_id": null,
"transcript_support_level": null,
"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": "ENST00000796454.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "HPN-AS1",
"gene_hgnc_id": 47041,
"hgvs_c": "n.329-2264A>G",
"hgvs_p": null,
"transcript": "ENST00000796455.1",
"protein_id": null,
"transcript_support_level": null,
"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": "ENST00000796455.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "HPN-AS1",
"gene_hgnc_id": 47041,
"hgvs_c": "n.236-2264A>G",
"hgvs_p": null,
"transcript": "ENST00000796456.1",
"protein_id": null,
"transcript_support_level": null,
"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": "ENST00000796456.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "HPN-AS1",
"gene_hgnc_id": 47041,
"hgvs_c": "n.306-2264A>G",
"hgvs_p": null,
"transcript": "ENST00000796457.1",
"protein_id": null,
"transcript_support_level": null,
"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": "ENST00000796457.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "HPN-AS1",
"gene_hgnc_id": 47041,
"hgvs_c": "n.379-2264A>G",
"hgvs_p": null,
"transcript": "ENST00000796458.1",
"protein_id": null,
"transcript_support_level": null,
"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": "ENST00000796458.1"
}
],
"gene_symbol": "SCN1B",
"gene_hgnc_id": 10586,
"dbsnp": null,
"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": 0.976154088973999,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.596,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.2,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 0.352,
"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": 11,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5",
"acmg_by_gene": [
{
"score": 11,
"benign_score": 0,
"pathogenic_score": 11,
"criteria": [
"PVS1",
"PM2",
"PP5"
],
"verdict": "Pathogenic",
"transcript": "NM_199037.5",
"gene_symbol": "SCN1B",
"hgnc_id": 10586,
"effects": [
"start_lost"
],
"inheritance_mode": "AD,Unknown,AR",
"hgvs_c": "c.2T>C",
"hgvs_p": "p.Met1?"
},
{
"score": 7,
"benign_score": 0,
"pathogenic_score": 7,
"criteria": [
"PM2",
"PP3_Strong",
"PP5"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000796454.1",
"gene_symbol": "HPN-AS1",
"hgnc_id": 47041,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.413-2264A>G",
"hgvs_p": null
}
],
"clinvar_disease": "Brugada syndrome 5,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "P:1 US:2",
"phenotype_combined": "not provided|Brugada syndrome 5",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}