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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: 2-219282062-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=219282062&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 219282062,
"ref": "G",
"alt": "A",
"effect": "splice_donor_variant,intron_variant",
"transcript": "NM_006736.6",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "DNAJB2",
"gene_hgnc_id": 5228,
"hgvs_c": "c.352+1G>A",
"hgvs_p": null,
"transcript": "NM_006736.6",
"protein_id": "NP_006727.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 324,
"cds_start": null,
"cds_end": null,
"cds_length": 975,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000336576.10",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_006736.6"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "DNAJB2",
"gene_hgnc_id": 5228,
"hgvs_c": "c.352+1G>A",
"hgvs_p": null,
"transcript": "ENST00000336576.10",
"protein_id": "ENSP00000338019.5",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 324,
"cds_start": null,
"cds_end": null,
"cds_length": 975,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_006736.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000336576.10"
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAJB2",
"gene_hgnc_id": 5228,
"hgvs_c": "c.353G>A",
"hgvs_p": "p.Gly118Asp",
"transcript": "ENST00000421532.5",
"protein_id": "ENSP00000395173.1",
"transcript_support_level": 2,
"aa_start": 118,
"aa_end": null,
"aa_length": 131,
"cds_start": 353,
"cds_end": null,
"cds_length": 396,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000421532.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "DNAJB2",
"gene_hgnc_id": 5228,
"hgvs_c": "c.352+1G>A",
"hgvs_p": null,
"transcript": "ENST00000933785.1",
"protein_id": "ENSP00000603844.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 324,
"cds_start": null,
"cds_end": null,
"cds_length": 975,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000933785.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "DNAJB2",
"gene_hgnc_id": 5228,
"hgvs_c": "c.352+1G>A",
"hgvs_p": null,
"transcript": "NM_001039550.2",
"protein_id": "NP_001034639.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 277,
"cds_start": null,
"cds_end": null,
"cds_length": 834,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001039550.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "DNAJB2",
"gene_hgnc_id": 5228,
"hgvs_c": "c.352+1G>A",
"hgvs_p": null,
"transcript": "ENST00000392086.8",
"protein_id": "ENSP00000375936.4",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 277,
"cds_start": null,
"cds_end": null,
"cds_length": 834,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000392086.8"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "DNAJB2",
"gene_hgnc_id": 5228,
"hgvs_c": "c.352+1G>A",
"hgvs_p": null,
"transcript": "ENST00000392087.6",
"protein_id": "ENSP00000375937.2",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 243,
"cds_start": null,
"cds_end": null,
"cds_length": 733,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000392087.6"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "DNAJB2",
"gene_hgnc_id": 5228,
"hgvs_c": "c.352+1G>A",
"hgvs_p": null,
"transcript": "ENST00000425450.5",
"protein_id": "ENSP00000414796.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 227,
"cds_start": null,
"cds_end": null,
"cds_length": 684,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000425450.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "DNAJB2",
"gene_hgnc_id": 5228,
"hgvs_c": "c.352+1G>A",
"hgvs_p": null,
"transcript": "ENST00000439026.1",
"protein_id": "ENSP00000387951.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 147,
"cds_start": null,
"cds_end": null,
"cds_length": 445,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000439026.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "DNAJB2",
"gene_hgnc_id": 5228,
"hgvs_c": "c.352+1G>A",
"hgvs_p": null,
"transcript": "ENST00000442681.5",
"protein_id": "ENSP00000392790.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 121,
"cds_start": null,
"cds_end": null,
"cds_length": 368,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000442681.5"
},
{
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAJB2",
"gene_hgnc_id": 5228,
"hgvs_c": "n.541G>A",
"hgvs_p": null,
"transcript": "ENST00000480537.5",
"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": "ENST00000480537.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "DNAJB2",
"gene_hgnc_id": 5228,
"hgvs_c": "n.343+1G>A",
"hgvs_p": null,
"transcript": "ENST00000463463.5",
"protein_id": null,
"transcript_support_level": 3,
"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": "ENST00000463463.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "DNAJB2",
"gene_hgnc_id": 5228,
"hgvs_c": "n.1570+1G>A",
"hgvs_p": null,
"transcript": "ENST00000477917.5",
"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": "ENST00000477917.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "DNAJB2",
"gene_hgnc_id": 5228,
"hgvs_c": "n.252+1G>A",
"hgvs_p": null,
"transcript": "ENST00000487855.1",
"protein_id": null,
"transcript_support_level": 3,
"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": "ENST00000487855.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "DNAJB2",
"gene_hgnc_id": 5228,
"hgvs_c": "n.1055+1G>A",
"hgvs_p": null,
"transcript": "ENST00000683651.1",
"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": "ENST00000683651.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "DNAJB2",
"gene_hgnc_id": 5228,
"hgvs_c": "n.559+1G>A",
"hgvs_p": null,
"transcript": "ENST00000684599.1",
"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": "ENST00000684599.1"
}
],
"gene_symbol": "DNAJB2",
"gene_hgnc_id": 5228,
"dbsnp": "rs756614404",
"frequency_reference_population": 0.000013011394,
"hom_count_reference_population": 0,
"allele_count_reference_population": 21,
"gnomad_exomes_af": 0.0000123135,
"gnomad_genomes_af": 0.0000197158,
"gnomad_exomes_ac": 18,
"gnomad_genomes_ac": 3,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.31200000643730164,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "REVEL",
"splice_score_selected": 0.9279999732971191,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": 0.312,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.1332,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.15,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 9.459,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.98,
"spliceai_max_prediction": "Pathogenic",
"dbscsnv_ada_score": 0.999992446697775,
"dbscsnv_ada_prediction": "Pathogenic",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 18,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1_Strong,PS3,PM2,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 18,
"benign_score": 0,
"pathogenic_score": 18,
"criteria": [
"PVS1_Strong",
"PS3",
"PM2",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "NM_006736.6",
"gene_symbol": "DNAJB2",
"hgnc_id": 5228,
"effects": [
"splice_donor_variant",
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.352+1G>A",
"hgvs_p": null
}
],
"clinvar_disease": " autosomal recessive 5, distal hereditary motor,Autosomal recessive distal spinal muscular atrophy 2,Charcot-Marie-Tooth disease,Charcot-Marie-Tooth disease X-linked dominant 1,DNAJB2-related disorder,Inborn genetic diseases,Neuronopathy,not provided",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:5",
"phenotype_combined": "Neuronopathy, distal hereditary motor, autosomal recessive 5|Charcot-Marie-Tooth disease|Charcot-Marie-Tooth disease X-linked dominant 1|not provided|DNAJB2-related disorder|Inborn genetic diseases|Autosomal recessive distal spinal muscular atrophy 2",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}