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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: 2-219281737-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=219281737&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 219281737,
"ref": "C",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "ENST00000336576.10",
"consequences": [
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAJB2",
"gene_hgnc_id": 5228,
"hgvs_c": "c.195C>T",
"hgvs_p": "p.Tyr65Tyr",
"transcript": "NM_006736.6",
"protein_id": "NP_006727.2",
"transcript_support_level": null,
"aa_start": 65,
"aa_end": null,
"aa_length": 324,
"cds_start": 195,
"cds_end": null,
"cds_length": 975,
"cdna_start": 384,
"cdna_end": null,
"cdna_length": 3072,
"mane_select": "ENST00000336576.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAJB2",
"gene_hgnc_id": 5228,
"hgvs_c": "c.195C>T",
"hgvs_p": "p.Tyr65Tyr",
"transcript": "ENST00000336576.10",
"protein_id": "ENSP00000338019.5",
"transcript_support_level": 1,
"aa_start": 65,
"aa_end": null,
"aa_length": 324,
"cds_start": 195,
"cds_end": null,
"cds_length": 975,
"cdna_start": 384,
"cdna_end": null,
"cdna_length": 3072,
"mane_select": "NM_006736.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAJB2",
"gene_hgnc_id": 5228,
"hgvs_c": "c.195C>T",
"hgvs_p": "p.Tyr65Tyr",
"transcript": "NM_001039550.2",
"protein_id": "NP_001034639.1",
"transcript_support_level": null,
"aa_start": 65,
"aa_end": null,
"aa_length": 277,
"cds_start": 195,
"cds_end": null,
"cds_length": 834,
"cdna_start": 384,
"cdna_end": null,
"cdna_length": 1921,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAJB2",
"gene_hgnc_id": 5228,
"hgvs_c": "c.195C>T",
"hgvs_p": "p.Tyr65Tyr",
"transcript": "ENST00000392086.8",
"protein_id": "ENSP00000375936.4",
"transcript_support_level": 2,
"aa_start": 65,
"aa_end": null,
"aa_length": 277,
"cds_start": 195,
"cds_end": null,
"cds_length": 834,
"cdna_start": 406,
"cdna_end": null,
"cdna_length": 1946,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAJB2",
"gene_hgnc_id": 5228,
"hgvs_c": "c.195C>T",
"hgvs_p": "p.Tyr65Tyr",
"transcript": "ENST00000392087.6",
"protein_id": "ENSP00000375937.2",
"transcript_support_level": 5,
"aa_start": 65,
"aa_end": null,
"aa_length": 243,
"cds_start": 195,
"cds_end": null,
"cds_length": 733,
"cdna_start": 285,
"cdna_end": null,
"cdna_length": 823,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAJB2",
"gene_hgnc_id": 5228,
"hgvs_c": "c.195C>T",
"hgvs_p": "p.Tyr65Tyr",
"transcript": "ENST00000425450.5",
"protein_id": "ENSP00000414796.1",
"transcript_support_level": 3,
"aa_start": 65,
"aa_end": null,
"aa_length": 227,
"cds_start": 195,
"cds_end": null,
"cds_length": 684,
"cdna_start": 339,
"cdna_end": null,
"cdna_length": 828,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAJB2",
"gene_hgnc_id": 5228,
"hgvs_c": "c.195C>T",
"hgvs_p": "p.Tyr65Tyr",
"transcript": "ENST00000439026.1",
"protein_id": "ENSP00000387951.1",
"transcript_support_level": 3,
"aa_start": 65,
"aa_end": null,
"aa_length": 147,
"cds_start": 195,
"cds_end": null,
"cds_length": 445,
"cdna_start": 402,
"cdna_end": null,
"cdna_length": 652,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAJB2",
"gene_hgnc_id": 5228,
"hgvs_c": "c.195C>T",
"hgvs_p": "p.Tyr65Tyr",
"transcript": "ENST00000421532.5",
"protein_id": "ENSP00000395173.1",
"transcript_support_level": 2,
"aa_start": 65,
"aa_end": null,
"aa_length": 131,
"cds_start": 195,
"cds_end": null,
"cds_length": 396,
"cdna_start": 384,
"cdna_end": null,
"cdna_length": 585,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAJB2",
"gene_hgnc_id": 5228,
"hgvs_c": "c.195C>T",
"hgvs_p": "p.Tyr65Tyr",
"transcript": "ENST00000442681.5",
"protein_id": "ENSP00000392790.1",
"transcript_support_level": 3,
"aa_start": 65,
"aa_end": null,
"aa_length": 121,
"cds_start": 195,
"cds_end": null,
"cds_length": 368,
"cdna_start": 513,
"cdna_end": null,
"cdna_length": 686,
"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": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAJB2",
"gene_hgnc_id": 5228,
"hgvs_c": "n.186C>T",
"hgvs_p": null,
"transcript": "ENST00000463463.5",
"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": 807,
"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": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAJB2",
"gene_hgnc_id": 5228,
"hgvs_c": "n.1413C>T",
"hgvs_p": null,
"transcript": "ENST00000477917.5",
"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": 4487,
"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": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAJB2",
"gene_hgnc_id": 5228,
"hgvs_c": "n.383C>T",
"hgvs_p": null,
"transcript": "ENST00000480537.5",
"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": 1139,
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAJB2",
"gene_hgnc_id": 5228,
"hgvs_c": "n.95C>T",
"hgvs_p": null,
"transcript": "ENST00000487855.1",
"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": 439,
"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": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAJB2",
"gene_hgnc_id": 5228,
"hgvs_c": "n.898C>T",
"hgvs_p": null,
"transcript": "ENST00000683651.1",
"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": 1282,
"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": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAJB2",
"gene_hgnc_id": 5228,
"hgvs_c": "n.402C>T",
"hgvs_p": null,
"transcript": "ENST00000684599.1",
"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": 2603,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "DNAJB2",
"gene_hgnc_id": 5228,
"dbsnp": "rs116719245",
"frequency_reference_population": 0.0015074685,
"hom_count_reference_population": 8,
"allele_count_reference_population": 2433,
"gnomad_exomes_af": 0.00154541,
"gnomad_genomes_af": 0.0011431,
"gnomad_exomes_ac": 2259,
"gnomad_genomes_ac": 174,
"gnomad_exomes_homalt": 6,
"gnomad_genomes_homalt": 2,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.5,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.5,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.799,
"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": -21,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BS1,BS2",
"acmg_by_gene": [
{
"score": -21,
"benign_score": 21,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000336576.10",
"gene_symbol": "DNAJB2",
"hgnc_id": 5228,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.195C>T",
"hgvs_p": "p.Tyr65Tyr"
}
],
"clinvar_disease": " autosomal recessive 5, distal hereditary motor,Charcot-Marie-Tooth disease,DNAJB2-related disorder,Inborn genetic diseases,Neuronopathy,not provided",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:6",
"phenotype_combined": "Neuronopathy, distal hereditary motor, autosomal recessive 5|Charcot-Marie-Tooth disease|not provided|Inborn genetic diseases|DNAJB2-related disorder",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}