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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: 19-12807328-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=12807328&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 12807328,
"ref": "C",
"alt": "G",
"effect": "missense_variant,splice_region_variant",
"transcript": "ENST00000221486.6",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RNASEH2A",
"gene_hgnc_id": 18518,
"hgvs_c": "c.322C>G",
"hgvs_p": "p.Arg108Gly",
"transcript": "NM_006397.3",
"protein_id": "NP_006388.2",
"transcript_support_level": null,
"aa_start": 108,
"aa_end": null,
"aa_length": 299,
"cds_start": 322,
"cds_end": null,
"cds_length": 900,
"cdna_start": 412,
"cdna_end": null,
"cdna_length": 1164,
"mane_select": "ENST00000221486.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "G",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RNASEH2A",
"gene_hgnc_id": 18518,
"hgvs_c": "c.322C>G",
"hgvs_p": "p.Arg108Gly",
"transcript": "ENST00000221486.6",
"protein_id": "ENSP00000221486.4",
"transcript_support_level": 1,
"aa_start": 108,
"aa_end": null,
"aa_length": 299,
"cds_start": 322,
"cds_end": null,
"cds_length": 900,
"cdna_start": 412,
"cdna_end": null,
"cdna_length": 1164,
"mane_select": "NM_006397.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RNASEH2A",
"gene_hgnc_id": 18518,
"hgvs_c": "c.319C>G",
"hgvs_p": "p.Arg107Gly",
"transcript": "ENST00000590121.2",
"protein_id": "ENSP00000495087.1",
"transcript_support_level": 2,
"aa_start": 107,
"aa_end": null,
"aa_length": 138,
"cds_start": 319,
"cds_end": null,
"cds_length": 417,
"cdna_start": 319,
"cdna_end": null,
"cdna_length": 878,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RNASEH2A",
"gene_hgnc_id": 18518,
"hgvs_c": "n.737C>G",
"hgvs_p": null,
"transcript": "ENST00000590279.2",
"protein_id": null,
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 823,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RNASEH2A",
"gene_hgnc_id": 18518,
"hgvs_c": "n.519C>G",
"hgvs_p": null,
"transcript": "ENST00000593017.2",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1245,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "THSD8",
"gene_hgnc_id": 53785,
"hgvs_c": "n.*201C>G",
"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": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1251,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RNASEH2A",
"gene_hgnc_id": 18518,
"hgvs_c": "n.357C>G",
"hgvs_p": null,
"transcript": "ENST00000643757.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 916,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "THSD8",
"gene_hgnc_id": 53785,
"hgvs_c": "n.*201C>G",
"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": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1251,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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+17850G>C",
"hgvs_p": null,
"transcript": "ENST00000589765.1",
"protein_id": null,
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 108,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "RNASEH2A",
"gene_hgnc_id": 18518,
"hgvs_c": "n.200-91C>G",
"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": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 714,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "RNASEH2A",
"gene_hgnc_id": 18518,
"dbsnp": "rs76436818",
"frequency_reference_population": 0.000042131665,
"hom_count_reference_population": 0,
"allele_count_reference_population": 68,
"gnomad_exomes_af": 0.0000430949,
"gnomad_genomes_af": 0.0000328735,
"gnomad_exomes_ac": 63,
"gnomad_genomes_ac": 5,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8789823055267334,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.3779999911785126,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": 0.738,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.5961,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.24,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 1.73,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.05,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.48499186044288,
"dbscsnv_ada_prediction": "Benign",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 4,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM5,PP3_Moderate",
"acmg_by_gene": [
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM5",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000221486.6",
"gene_symbol": "RNASEH2A",
"hgnc_id": 18518,
"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.322C>G",
"hgvs_p": "p.Arg108Gly"
},
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000639767.2",
"gene_symbol": "THSD8",
"hgnc_id": 53785,
"effects": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.*201C>G",
"hgvs_p": null
},
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000589765.1",
"gene_symbol": "HOOK2",
"hgnc_id": 19885,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "n.41+17850G>C",
"hgvs_p": null
}
],
"clinvar_disease": "Aicardi-Goutieres syndrome 4,not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:2",
"phenotype_combined": "Aicardi-Goutieres syndrome 4|not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}