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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: 2-219284842-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=219284842&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 219284842,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000336576.10",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAJB2",
"gene_hgnc_id": 5228,
"hgvs_c": "c.830G>A",
"hgvs_p": "p.Arg277Gln",
"transcript": "NM_006736.6",
"protein_id": "NP_006727.2",
"transcript_support_level": null,
"aa_start": 277,
"aa_end": null,
"aa_length": 324,
"cds_start": 830,
"cds_end": null,
"cds_length": 975,
"cdna_start": 1019,
"cdna_end": null,
"cdna_length": 3072,
"mane_select": "ENST00000336576.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAJB2",
"gene_hgnc_id": 5228,
"hgvs_c": "c.830G>A",
"hgvs_p": "p.Arg277Gln",
"transcript": "ENST00000336576.10",
"protein_id": "ENSP00000338019.5",
"transcript_support_level": 1,
"aa_start": 277,
"aa_end": null,
"aa_length": 324,
"cds_start": 830,
"cds_end": null,
"cds_length": 975,
"cdna_start": 1019,
"cdna_end": null,
"cdna_length": 3072,
"mane_select": "NM_006736.6",
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAJB2",
"gene_hgnc_id": 5228,
"hgvs_c": "n.617G>A",
"hgvs_p": null,
"transcript": "ENST00000473750.5",
"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": 971,
"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": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAJB2",
"gene_hgnc_id": 5228,
"hgvs_c": "n.454G>A",
"hgvs_p": null,
"transcript": "ENST00000476254.1",
"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": 486,
"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": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAJB2",
"gene_hgnc_id": 5228,
"hgvs_c": "n.2434G>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": -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": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAJB2",
"gene_hgnc_id": 5228,
"hgvs_c": "n.1037G>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": -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
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "DNAJB2",
"gene_hgnc_id": 5228,
"hgvs_c": "c.823+7G>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": -4,
"cds_end": null,
"cds_length": 834,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1921,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "DNAJB2",
"gene_hgnc_id": 5228,
"hgvs_c": "c.823+7G>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": -4,
"cds_end": null,
"cds_length": 834,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1946,
"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",
"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": "n.566+7G>A",
"hgvs_p": null,
"transcript": "ENST00000472019.5",
"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": 1419,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAJB2",
"gene_hgnc_id": 5228,
"hgvs_c": "c.*4G>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": -4,
"cds_end": null,
"cds_length": 733,
"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": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAJB2",
"gene_hgnc_id": 5228,
"hgvs_c": "c.*146G>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": -4,
"cds_end": null,
"cds_length": 684,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 828,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAJB2",
"gene_hgnc_id": 5228,
"hgvs_c": "n.*14G>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": -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
}
],
"gene_symbol": "DNAJB2",
"gene_hgnc_id": 5228,
"dbsnp": "rs778963579",
"frequency_reference_population": 0.0000068270233,
"hom_count_reference_population": 0,
"allele_count_reference_population": 11,
"gnomad_exomes_af": 0.00000616854,
"gnomad_genomes_af": 0.0000131382,
"gnomad_exomes_ac": 9,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.09152877330780029,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.07999999821186066,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.164,
"revel_prediction": "Benign",
"alphamissense_score": 0.0827,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.26,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.186,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.08,
"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": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Moderate,BP6_Moderate",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate",
"BP6_Moderate"
],
"verdict": "Likely_benign",
"transcript": "ENST00000336576.10",
"gene_symbol": "DNAJB2",
"hgnc_id": 5228,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.830G>A",
"hgvs_p": "p.Arg277Gln"
}
],
"clinvar_disease": " autosomal recessive 5, distal hereditary motor,Neuronopathy",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "Neuronopathy, distal hereditary motor, autosomal recessive 5",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}