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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: 1-8656284-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=8656284&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 8656284,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000400908.7",
"consequences": [
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RERE",
"gene_hgnc_id": 9965,
"hgvs_c": "c.14A>G",
"hgvs_p": "p.Lys5Arg",
"transcript": "NM_001042681.2",
"protein_id": "NP_001036146.1",
"transcript_support_level": null,
"aa_start": 5,
"aa_end": null,
"aa_length": 1566,
"cds_start": 14,
"cds_end": null,
"cds_length": 4701,
"cdna_start": 639,
"cdna_end": null,
"cdna_length": 8009,
"mane_select": "ENST00000400908.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RERE",
"gene_hgnc_id": 9965,
"hgvs_c": "c.14A>G",
"hgvs_p": "p.Lys5Arg",
"transcript": "ENST00000400908.7",
"protein_id": "ENSP00000383700.2",
"transcript_support_level": 1,
"aa_start": 5,
"aa_end": null,
"aa_length": 1566,
"cds_start": 14,
"cds_end": null,
"cds_length": 4701,
"cdna_start": 639,
"cdna_end": null,
"cdna_length": 8009,
"mane_select": "NM_001042681.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RERE",
"gene_hgnc_id": 9965,
"hgvs_c": "c.14A>G",
"hgvs_p": "p.Lys5Arg",
"transcript": "ENST00000337907.7",
"protein_id": "ENSP00000338629.3",
"transcript_support_level": 1,
"aa_start": 5,
"aa_end": null,
"aa_length": 1566,
"cds_start": 14,
"cds_end": null,
"cds_length": 4701,
"cdna_start": 649,
"cdna_end": null,
"cdna_length": 8026,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RERE",
"gene_hgnc_id": 9965,
"hgvs_c": "c.14A>G",
"hgvs_p": "p.Lys5Arg",
"transcript": "NM_012102.4",
"protein_id": "NP_036234.3",
"transcript_support_level": null,
"aa_start": 5,
"aa_end": null,
"aa_length": 1566,
"cds_start": 14,
"cds_end": null,
"cds_length": 4701,
"cdna_start": 824,
"cdna_end": null,
"cdna_length": 8194,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RERE",
"gene_hgnc_id": 9965,
"hgvs_c": "c.14A>G",
"hgvs_p": "p.Lys5Arg",
"transcript": "ENST00000656437.1",
"protein_id": "ENSP00000499322.1",
"transcript_support_level": null,
"aa_start": 5,
"aa_end": null,
"aa_length": 782,
"cds_start": 14,
"cds_end": null,
"cds_length": 2349,
"cdna_start": 1239,
"cdna_end": null,
"cdna_length": 3574,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RERE",
"gene_hgnc_id": 9965,
"hgvs_c": "c.14A>G",
"hgvs_p": "p.Lys5Arg",
"transcript": "ENST00000400907.6",
"protein_id": "ENSP00000383699.2",
"transcript_support_level": 5,
"aa_start": 5,
"aa_end": null,
"aa_length": 584,
"cds_start": 14,
"cds_end": null,
"cds_length": 1755,
"cdna_start": 88,
"cdna_end": null,
"cdna_length": 2973,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RERE",
"gene_hgnc_id": 9965,
"hgvs_c": "c.14A>G",
"hgvs_p": "p.Lys5Arg",
"transcript": "ENST00000659924.1",
"protein_id": "ENSP00000499704.1",
"transcript_support_level": null,
"aa_start": 5,
"aa_end": null,
"aa_length": 402,
"cds_start": 14,
"cds_end": null,
"cds_length": 1209,
"cdna_start": 270,
"cdna_end": null,
"cdna_length": 2990,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RERE",
"gene_hgnc_id": 9965,
"hgvs_c": "c.14A>G",
"hgvs_p": "p.Lys5Arg",
"transcript": "ENST00000704050.1",
"protein_id": "ENSP00000515653.1",
"transcript_support_level": null,
"aa_start": 5,
"aa_end": null,
"aa_length": 101,
"cds_start": 14,
"cds_end": null,
"cds_length": 306,
"cdna_start": 263,
"cdna_end": null,
"cdna_length": 555,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RERE",
"gene_hgnc_id": 9965,
"hgvs_c": "c.14A>G",
"hgvs_p": "p.Lys5Arg",
"transcript": "ENST00000468247.1",
"protein_id": "ENSP00000465271.1",
"transcript_support_level": 2,
"aa_start": 5,
"aa_end": null,
"aa_length": 34,
"cds_start": 14,
"cds_end": null,
"cds_length": 105,
"cdna_start": 323,
"cdna_end": null,
"cdna_length": 414,
"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": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RERE",
"gene_hgnc_id": 9965,
"hgvs_c": "n.566A>G",
"hgvs_p": null,
"transcript": "ENST00000480342.5",
"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": 2710,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "RERE",
"gene_hgnc_id": 9965,
"dbsnp": "rs1553128615",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.3126348853111267,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.195,
"revel_prediction": "Benign",
"alphamissense_score": 0.121,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.24,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 7.619,
"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": "ENST00000400908.7",
"gene_symbol": "RERE",
"hgnc_id": 9965,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.14A>G",
"hgvs_p": "p.Lys5Arg"
}
],
"clinvar_disease": " eye, or heart,Neurodevelopmental disorder with or without anomalies of the brain",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Neurodevelopmental disorder with or without anomalies of the brain, eye, or heart",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}