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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: 19-12813191-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=12813191&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 12813191,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_006397.3",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RNASEH2A",
"gene_hgnc_id": 18518,
"hgvs_c": "c.746C>T",
"hgvs_p": "p.Ala249Val",
"transcript": "NM_006397.3",
"protein_id": "NP_006388.2",
"transcript_support_level": null,
"aa_start": 249,
"aa_end": null,
"aa_length": 299,
"cds_start": 746,
"cds_end": null,
"cds_length": 900,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000221486.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_006397.3"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RNASEH2A",
"gene_hgnc_id": 18518,
"hgvs_c": "c.746C>T",
"hgvs_p": "p.Ala249Val",
"transcript": "ENST00000221486.6",
"protein_id": "ENSP00000221486.4",
"transcript_support_level": 1,
"aa_start": 249,
"aa_end": null,
"aa_length": 299,
"cds_start": 746,
"cds_end": null,
"cds_length": 900,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_006397.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000221486.6"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RNASEH2A",
"gene_hgnc_id": 18518,
"hgvs_c": "c.716C>T",
"hgvs_p": "p.Ala239Val",
"transcript": "ENST00000926045.1",
"protein_id": "ENSP00000596104.1",
"transcript_support_level": null,
"aa_start": 239,
"aa_end": null,
"aa_length": 289,
"cds_start": 716,
"cds_end": null,
"cds_length": 870,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000926045.1"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RNASEH2A",
"gene_hgnc_id": 18518,
"hgvs_c": "c.698C>T",
"hgvs_p": "p.Ala233Val",
"transcript": "ENST00000926044.1",
"protein_id": "ENSP00000596103.1",
"transcript_support_level": null,
"aa_start": 233,
"aa_end": null,
"aa_length": 283,
"cds_start": 698,
"cds_end": null,
"cds_length": 852,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000926044.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RNASEH2A",
"gene_hgnc_id": 18518,
"hgvs_c": "n.1032C>T",
"hgvs_p": null,
"transcript": "ENST00000593017.2",
"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": "retained_intron",
"feature": "ENST00000593017.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "THSD8",
"gene_hgnc_id": 53785,
"hgvs_c": "n.*625C>T",
"hgvs_p": null,
"transcript": "ENST00000639767.2",
"protein_id": "ENSP00000491410.2",
"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": "nonsense_mediated_decay",
"feature": "ENST00000639767.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RNASEH2A",
"gene_hgnc_id": 18518,
"hgvs_c": "n.781C>T",
"hgvs_p": null,
"transcript": "ENST00000643757.1",
"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": "retained_intron",
"feature": "ENST00000643757.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RNASEH2A",
"gene_hgnc_id": 18518,
"hgvs_c": "n.*406C>T",
"hgvs_p": null,
"transcript": "ENST00000646769.1",
"protein_id": "ENSP00000495175.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000646769.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "THSD8",
"gene_hgnc_id": 53785,
"hgvs_c": "n.*625C>T",
"hgvs_p": null,
"transcript": "ENST00000639767.2",
"protein_id": "ENSP00000491410.2",
"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": "nonsense_mediated_decay",
"feature": "ENST00000639767.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RNASEH2A",
"gene_hgnc_id": 18518,
"hgvs_c": "n.*406C>T",
"hgvs_p": null,
"transcript": "ENST00000646769.1",
"protein_id": "ENSP00000495175.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000646769.1"
},
{
"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": 3,
"intron_rank_end": null,
"gene_symbol": "HOOK2",
"gene_hgnc_id": 19885,
"hgvs_c": "n.41+11987G>A",
"hgvs_p": null,
"transcript": "ENST00000589765.1",
"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": "ENST00000589765.1"
}
],
"gene_symbol": "RNASEH2A",
"gene_hgnc_id": 18518,
"dbsnp": "rs758719669",
"frequency_reference_population": 0.00005453002,
"hom_count_reference_population": 0,
"allele_count_reference_population": 88,
"gnomad_exomes_af": 0.0000499405,
"gnomad_genomes_af": 0.0000986518,
"gnomad_exomes_ac": 73,
"gnomad_genomes_ac": 15,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.6559209227561951,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.10999999940395355,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.387,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.245,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.14,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 3.201,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.11,
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 0,
"pathogenic_score": 0,
"criteria": [],
"verdict": "Uncertain_significance",
"transcript": "NM_006397.3",
"gene_symbol": "RNASEH2A",
"hgnc_id": 18518,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.746C>T",
"hgvs_p": "p.Ala249Val"
},
{
"score": 0,
"benign_score": 0,
"pathogenic_score": 0,
"criteria": [],
"verdict": "Uncertain_significance",
"transcript": "ENST00000639767.2",
"gene_symbol": "THSD8",
"hgnc_id": 53785,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.*625C>T",
"hgvs_p": null
},
{
"score": 0,
"benign_score": 0,
"pathogenic_score": 0,
"criteria": [],
"verdict": "Uncertain_significance",
"transcript": "ENST00000589765.1",
"gene_symbol": "HOOK2",
"hgnc_id": 19885,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "n.41+11987G>A",
"hgvs_p": null
}
],
"clinvar_disease": "Aicardi-Goutieres syndrome 4,Inborn genetic diseases,RNASEH2A-related disorder,not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "LP:1 US:7",
"phenotype_combined": "Aicardi-Goutieres syndrome 4|Inborn genetic diseases|RNASEH2A-related disorder|not specified|not provided",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}