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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: 1-92837628-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=92837628&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 92837628,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000370321.8",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPL5",
"gene_hgnc_id": 10360,
"hgvs_c": "c.700G>A",
"hgvs_p": "p.Asp234Asn",
"transcript": "NM_000969.5",
"protein_id": "NP_000960.2",
"transcript_support_level": null,
"aa_start": 234,
"aa_end": null,
"aa_length": 297,
"cds_start": 700,
"cds_end": null,
"cds_length": 894,
"cdna_start": 775,
"cdna_end": null,
"cdna_length": 1028,
"mane_select": "ENST00000370321.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPL5",
"gene_hgnc_id": 10360,
"hgvs_c": "c.700G>A",
"hgvs_p": "p.Asp234Asn",
"transcript": "ENST00000370321.8",
"protein_id": "ENSP00000359345.2",
"transcript_support_level": 1,
"aa_start": 234,
"aa_end": null,
"aa_length": 297,
"cds_start": 700,
"cds_end": null,
"cds_length": 894,
"cdna_start": 775,
"cdna_end": null,
"cdna_length": 1028,
"mane_select": "NM_000969.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "DIPK1A",
"gene_hgnc_id": 32213,
"hgvs_c": "c.475-4594C>T",
"hgvs_p": null,
"transcript": "ENST00000615519.4",
"protein_id": "ENSP00000483279.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 162,
"cds_start": -4,
"cds_end": null,
"cds_length": 489,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 865,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPL5",
"gene_hgnc_id": 10360,
"hgvs_c": "c.550G>A",
"hgvs_p": "p.Asp184Asn",
"transcript": "ENST00000645300.1",
"protein_id": "ENSP00000495589.1",
"transcript_support_level": null,
"aa_start": 184,
"aa_end": null,
"aa_length": 237,
"cds_start": 550,
"cds_end": null,
"cds_length": 714,
"cdna_start": 732,
"cdna_end": null,
"cdna_length": 896,
"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": "RPL5",
"gene_hgnc_id": 10360,
"hgvs_c": "n.1019G>A",
"hgvs_p": null,
"transcript": "ENST00000497519.1",
"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": 1210,
"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": "RPL5",
"gene_hgnc_id": 10360,
"hgvs_c": "n.434G>A",
"hgvs_p": null,
"transcript": "ENST00000645908.1",
"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": 591,
"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": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPL5",
"gene_hgnc_id": 10360,
"hgvs_c": "n.759G>A",
"hgvs_p": null,
"transcript": "NR_146333.1",
"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": 1012,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "RPL5",
"gene_hgnc_id": 10360,
"hgvs_c": "c.324+2715G>A",
"hgvs_p": null,
"transcript": "ENST00000645119.1",
"protein_id": "ENSP00000493811.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 170,
"cds_start": -4,
"cds_end": null,
"cds_length": 513,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 629,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "DIPK1A",
"gene_hgnc_id": 32213,
"hgvs_c": "c.475-4594C>T",
"hgvs_p": null,
"transcript": "NM_001252273.2",
"protein_id": "NP_001239202.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 162,
"cds_start": -4,
"cds_end": null,
"cds_length": 489,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 813,
"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": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPL5",
"gene_hgnc_id": 10360,
"hgvs_c": "c.*159G>A",
"hgvs_p": null,
"transcript": "ENST00000315741.5",
"protein_id": "ENSP00000359338.2",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 129,
"cds_start": -4,
"cds_end": null,
"cds_length": 391,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 681,
"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": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SNORD21",
"gene_hgnc_id": 10144,
"hgvs_c": "n.*245G>A",
"hgvs_p": null,
"transcript": "ENST00000383953.1",
"protein_id": null,
"transcript_support_level": 6,
"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": 95,
"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": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SNORD21",
"gene_hgnc_id": 10144,
"hgvs_c": "n.*245G>A",
"hgvs_p": null,
"transcript": "NR_000006.8",
"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": 95,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "RPL5",
"gene_hgnc_id": 10360,
"dbsnp": "rs938367538",
"frequency_reference_population": 6.851295e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.8513e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.3526146411895752,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.201,
"revel_prediction": "Benign",
"alphamissense_score": 0.5665,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.34,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 9.733,
"phylop100way_prediction": "Pathogenic",
"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": 1,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4",
"acmg_by_gene": [
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000370321.8",
"gene_symbol": "RPL5",
"hgnc_id": 10360,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.700G>A",
"hgvs_p": "p.Asp234Asn"
},
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "NM_001252273.2",
"gene_symbol": "DIPK1A",
"hgnc_id": 32213,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.475-4594C>T",
"hgvs_p": null
},
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "NR_000006.8",
"gene_symbol": "SNORD21",
"hgnc_id": 10144,
"effects": [
"downstream_gene_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.*245G>A",
"hgvs_p": null
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}