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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: 19-35039667-A-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=35039667&ref=A&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PP3_Moderate",
"PP5"
],
"effects": [
"missense_variant"
],
"gene_symbol": "SCN1B",
"hgnc_id": 10586,
"hgvs_c": "c.623A>T",
"hgvs_p": "p.Lys208Ile",
"inheritance_mode": "AD,AR,Unknown",
"pathogenic_score": 3,
"score": 3,
"transcript": "NM_001037.5",
"verdict": "Uncertain_significance"
},
{
"benign_score": 0,
"criteria": [
"PM2",
"PP3_Moderate",
"PP5"
],
"effects": [
"intron_variant"
],
"gene_symbol": "HPN-AS1",
"hgnc_id": 47041,
"hgvs_c": "n.413-11109T>A",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 5,
"score": 5,
"transcript": "ENST00000796454.1",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PP3_Moderate,PP5",
"acmg_score": 3,
"allele_count_reference_population": 21,
"alphamissense_prediction": null,
"alphamissense_score": 0.9866,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.18,
"chr": "19",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_disease": "Brugada syndrome,Brugada syndrome 5,Cardiovascular phenotype,SCN1B-related disorder",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "LP:1 US:2 O:1",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.8525317907333374,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 218,
"aa_ref": "K",
"aa_start": 208,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1666,
"cdna_start": 974,
"cds_end": null,
"cds_length": 657,
"cds_start": 623,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "NM_001037.5",
"gene_hgnc_id": 10586,
"gene_symbol": "SCN1B",
"hgvs_c": "c.623A>T",
"hgvs_p": "p.Lys208Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000262631.11",
"protein_coding": true,
"protein_id": "NP_001028.1",
"strand": true,
"transcript": "NM_001037.5",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 218,
"aa_ref": "K",
"aa_start": 208,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 1666,
"cdna_start": 974,
"cds_end": null,
"cds_length": 657,
"cds_start": 623,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000262631.11",
"gene_hgnc_id": 10586,
"gene_symbol": "SCN1B",
"hgvs_c": "c.623A>T",
"hgvs_p": "p.Lys208Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001037.5",
"protein_coding": true,
"protein_id": "ENSP00000262631.3",
"strand": true,
"transcript": "ENST00000262631.11",
"transcript_support_level": 1
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 218,
"aa_ref": "K",
"aa_start": 208,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1600,
"cdna_start": 818,
"cds_end": null,
"cds_length": 657,
"cds_start": 623,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000638536.1",
"gene_hgnc_id": 10586,
"gene_symbol": "SCN1B",
"hgvs_c": "c.623A>T",
"hgvs_p": "p.Lys208Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000492022.1",
"strand": true,
"transcript": "ENST00000638536.1",
"transcript_support_level": 1
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 227,
"aa_ref": "K",
"aa_start": 217,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1612,
"cdna_start": 920,
"cds_end": null,
"cds_length": 684,
"cds_start": 650,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000675741.1",
"gene_hgnc_id": 10586,
"gene_symbol": "SCN1B",
"hgvs_c": "c.650A>T",
"hgvs_p": "p.Lys217Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000502395.1",
"strand": true,
"transcript": "ENST00000675741.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 191,
"aa_ref": "K",
"aa_start": 181,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1614,
"cdna_start": 916,
"cds_end": null,
"cds_length": 576,
"cds_start": 542,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000955983.1",
"gene_hgnc_id": 10586,
"gene_symbol": "SCN1B",
"hgvs_c": "c.542A>T",
"hgvs_p": "p.Lys181Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000626042.1",
"strand": true,
"transcript": "ENST00000955983.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 185,
"aa_ref": "K",
"aa_start": 175,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1785,
"cdna_start": 1093,
"cds_end": null,
"cds_length": 558,
"cds_start": 524,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "NM_001321605.2",
"gene_hgnc_id": 10586,
"gene_symbol": "SCN1B",
"hgvs_c": "c.524A>T",
"hgvs_p": "p.Lys175Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001308534.1",
"strand": true,
"transcript": "NM_001321605.2",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 185,
"aa_ref": "K",
"aa_start": 175,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1176,
"cdna_start": 1011,
"cds_end": null,
"cds_length": 558,
"cds_start": 524,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000596348.2",
"gene_hgnc_id": 10586,
"gene_symbol": "SCN1B",
"hgvs_c": "c.524A>T",
"hgvs_p": "p.Lys175Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000492247.1",
"strand": true,
"transcript": "ENST00000596348.2",
"transcript_support_level": 5
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 147,
"aa_ref": "K",
"aa_start": 137,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 814,
"cdna_start": 498,
"cds_end": null,
"cds_length": 444,
"cds_start": 410,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000595652.5",
"gene_hgnc_id": 10586,
"gene_symbol": "SCN1B",
"hgvs_c": "c.410A>T",
"hgvs_p": "p.Lys137Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000468848.1",
"strand": true,
"transcript": "ENST00000595652.5",
"transcript_support_level": 2
},
{
"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": 3461,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 2,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000602150.2",
"gene_hgnc_id": 10586,
"gene_symbol": "SCN1B",
"hgvs_c": "n.2769A>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000602150.2",
"transcript_support_level": 2
},
{
"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": 1804,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 7,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000676410.1",
"gene_hgnc_id": 10586,
"gene_symbol": "SCN1B",
"hgvs_c": "n.*341A>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000502717.1",
"strand": true,
"transcript": "ENST00000676410.1",
"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": 1804,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 7,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000676410.1",
"gene_hgnc_id": 10586,
"gene_symbol": "SCN1B",
"hgvs_c": "n.*341A>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000502717.1",
"strand": true,
"transcript": "ENST00000676410.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 1017,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000796454.1",
"gene_hgnc_id": 47041,
"gene_symbol": "HPN-AS1",
"hgvs_c": "n.413-11109T>A",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000796454.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 935,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000796455.1",
"gene_hgnc_id": 47041,
"gene_symbol": "HPN-AS1",
"hgvs_c": "n.329-11109T>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000796455.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 842,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000796456.1",
"gene_hgnc_id": 47041,
"gene_symbol": "HPN-AS1",
"hgvs_c": "n.236-11109T>A",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000796456.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 912,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000796457.1",
"gene_hgnc_id": 47041,
"gene_symbol": "HPN-AS1",
"hgvs_c": "n.306-11109T>A",
"hgvs_p": null,
"intron_rank": 3,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000796457.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 985,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000796458.1",
"gene_hgnc_id": 47041,
"gene_symbol": "HPN-AS1",
"hgvs_c": "n.379-11109T>A",
"hgvs_p": null,
"intron_rank": 3,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000796458.1",
"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": 1430,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000639260.1",
"gene_hgnc_id": 10586,
"gene_symbol": "SCN1B",
"hgvs_c": "n.*6A>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000639260.1",
"transcript_support_level": 3
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs780958012",
"effect": "missense_variant",
"frequency_reference_population": 0.000013010685,
"gene_hgnc_id": 10586,
"gene_symbol": "SCN1B",
"gnomad_exomes_ac": 18,
"gnomad_exomes_af": 0.0000123129,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 3,
"gnomad_genomes_af": 0.0000197143,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"phenotype_combined": "Brugada syndrome 5|SCN1B-related disorder|Cardiovascular phenotype|Brugada syndrome",
"phylop100way_prediction": "Pathogenic",
"phylop100way_score": 8.346,
"pos": 35039667,
"ref": "A",
"revel_prediction": "Pathogenic",
"revel_score": 0.873,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_001037.5"
}
]
}