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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: 2-3550413-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=3550413&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 3550413,
"ref": "G",
"alt": "A",
"effect": "stop_gained",
"transcript": "ENST00000315212.4",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RNASEH1",
"gene_hgnc_id": 18466,
"hgvs_c": "c.469C>T",
"hgvs_p": "p.Arg157*",
"transcript": "NM_002936.6",
"protein_id": "NP_002927.2",
"transcript_support_level": null,
"aa_start": 157,
"aa_end": null,
"aa_length": 286,
"cds_start": 469,
"cds_end": null,
"cds_length": 861,
"cdna_start": 542,
"cdna_end": null,
"cdna_length": 5289,
"mane_select": "ENST00000315212.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RNASEH1",
"gene_hgnc_id": 18466,
"hgvs_c": "c.469C>T",
"hgvs_p": "p.Arg157*",
"transcript": "ENST00000315212.4",
"protein_id": "ENSP00000313350.3",
"transcript_support_level": 1,
"aa_start": 157,
"aa_end": null,
"aa_length": 286,
"cds_start": 469,
"cds_end": null,
"cds_length": 861,
"cdna_start": 542,
"cdna_end": null,
"cdna_length": 5289,
"mane_select": "NM_002936.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000286905",
"gene_hgnc_id": null,
"hgvs_c": "n.469C>T",
"hgvs_p": null,
"transcript": "ENST00000658393.1",
"protein_id": "ENSP00000499330.1",
"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": 2742,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RNASEH1",
"gene_hgnc_id": 18466,
"hgvs_c": "c.466C>T",
"hgvs_p": "p.Arg156*",
"transcript": "NM_001378272.1",
"protein_id": "NP_001365201.1",
"transcript_support_level": null,
"aa_start": 156,
"aa_end": null,
"aa_length": 285,
"cds_start": 466,
"cds_end": null,
"cds_length": 858,
"cdna_start": 539,
"cdna_end": null,
"cdna_length": 5286,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RNASEH1",
"gene_hgnc_id": 18466,
"hgvs_c": "c.469C>T",
"hgvs_p": "p.Arg157*",
"transcript": "NM_001378273.1",
"protein_id": "NP_001365202.1",
"transcript_support_level": null,
"aa_start": 157,
"aa_end": null,
"aa_length": 281,
"cds_start": 469,
"cds_end": null,
"cds_length": 846,
"cdna_start": 542,
"cdna_end": null,
"cdna_length": 5274,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RNASEH1",
"gene_hgnc_id": 18466,
"hgvs_c": "c.469C>T",
"hgvs_p": "p.Arg157*",
"transcript": "NM_001378271.1",
"protein_id": "NP_001365200.1",
"transcript_support_level": null,
"aa_start": 157,
"aa_end": null,
"aa_length": 274,
"cds_start": 469,
"cds_end": null,
"cds_length": 825,
"cdna_start": 542,
"cdna_end": null,
"cdna_length": 5309,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RNASEH1",
"gene_hgnc_id": 18466,
"hgvs_c": "c.391C>T",
"hgvs_p": "p.Arg131*",
"transcript": "NM_001286834.3",
"protein_id": "NP_001273763.1",
"transcript_support_level": null,
"aa_start": 131,
"aa_end": null,
"aa_length": 260,
"cds_start": 391,
"cds_end": null,
"cds_length": 783,
"cdna_start": 542,
"cdna_end": null,
"cdna_length": 5289,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RNASEH1",
"gene_hgnc_id": 18466,
"hgvs_c": "c.118C>T",
"hgvs_p": "p.Arg40*",
"transcript": "NM_001286837.3",
"protein_id": "NP_001273766.1",
"transcript_support_level": null,
"aa_start": 40,
"aa_end": null,
"aa_length": 169,
"cds_start": 118,
"cds_end": null,
"cds_length": 510,
"cdna_start": 780,
"cdna_end": null,
"cdna_length": 5527,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RNASEH1",
"gene_hgnc_id": 18466,
"hgvs_c": "n.*575C>T",
"hgvs_p": null,
"transcript": "ENST00000436842.5",
"protein_id": "ENSP00000404926.1",
"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": 2120,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RNASEH1",
"gene_hgnc_id": 18466,
"hgvs_c": "n.*506C>T",
"hgvs_p": null,
"transcript": "ENST00000454734.1",
"protein_id": "ENSP00000411646.1",
"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": 749,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RNASEH1",
"gene_hgnc_id": 18466,
"hgvs_c": "n.225C>T",
"hgvs_p": null,
"transcript": "ENST00000464986.5",
"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": 514,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000286905",
"gene_hgnc_id": null,
"hgvs_c": "n.469C>T",
"hgvs_p": null,
"transcript": "ENST00000654051.1",
"protein_id": "ENSP00000499604.1",
"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": 2657,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RNASEH1",
"gene_hgnc_id": 18466,
"hgvs_c": "n.542C>T",
"hgvs_p": null,
"transcript": "NR_148532.2",
"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": 2852,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RNASEH1",
"gene_hgnc_id": 18466,
"hgvs_c": "n.542C>T",
"hgvs_p": null,
"transcript": "NR_148533.2",
"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": 5285,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RNASEH1",
"gene_hgnc_id": 18466,
"hgvs_c": "n.542C>T",
"hgvs_p": null,
"transcript": "NR_148534.2",
"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": 2968,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RNASEH1",
"gene_hgnc_id": 18466,
"hgvs_c": "n.426C>T",
"hgvs_p": null,
"transcript": "NR_165465.1",
"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": 5173,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RNASEH1",
"gene_hgnc_id": 18466,
"hgvs_c": "n.542C>T",
"hgvs_p": null,
"transcript": "NR_165466.1",
"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": 5258,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RNASEH1",
"gene_hgnc_id": 18466,
"hgvs_c": "n.711C>T",
"hgvs_p": null,
"transcript": "NR_165467.1",
"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": 5458,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RNASEH1",
"gene_hgnc_id": 18466,
"hgvs_c": "n.514C>T",
"hgvs_p": null,
"transcript": "NR_165468.1",
"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": 5261,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RNASEH1",
"gene_hgnc_id": 18466,
"hgvs_c": "n.*575C>T",
"hgvs_p": null,
"transcript": "ENST00000436842.5",
"protein_id": "ENSP00000404926.1",
"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": 2120,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RNASEH1",
"gene_hgnc_id": 18466,
"hgvs_c": "n.*506C>T",
"hgvs_p": null,
"transcript": "ENST00000454734.1",
"protein_id": "ENSP00000411646.1",
"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": 749,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "RNASEH1",
"gene_hgnc_id": 18466,
"dbsnp": "rs373442996",
"frequency_reference_population": 0.000004956814,
"hom_count_reference_population": 0,
"allele_count_reference_population": 8,
"gnomad_exomes_af": 0.0000041044,
"gnomad_genomes_af": 0.0000131498,
"gnomad_exomes_ac": 6,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.5400000214576721,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.54,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 3.419,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.01,
"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": 10,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PP5_Moderate",
"acmg_by_gene": [
{
"score": 10,
"benign_score": 0,
"pathogenic_score": 10,
"criteria": [
"PVS1",
"PP5_Moderate"
],
"verdict": "Pathogenic",
"transcript": "ENST00000315212.4",
"gene_symbol": "RNASEH1",
"hgnc_id": 18466,
"effects": [
"stop_gained"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.469C>T",
"hgvs_p": "p.Arg157*"
},
{
"score": 8,
"benign_score": 0,
"pathogenic_score": 8,
"criteria": [
"PM2",
"PP3_Strong",
"PP5_Moderate"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000658393.1",
"gene_symbol": "ENSG00000286905",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.469C>T",
"hgvs_p": null
}
],
"clinvar_disease": " autosomal recessive 2,Progressive external ophthalmoplegia with mitochondrial DNA deletions,not provided",
"clinvar_classification": "Likely pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LP:1",
"phenotype_combined": "Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal recessive 2|not provided",
"pathogenicity_classification_combined": "Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}