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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: 19-50479052-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=50479052&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 50479052,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_206538.4",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EMC10",
"gene_hgnc_id": 27609,
"hgvs_c": "c.283C>T",
"hgvs_p": "p.Arg95Trp",
"transcript": "NM_206538.4",
"protein_id": "NP_996261.1",
"transcript_support_level": null,
"aa_start": 95,
"aa_end": null,
"aa_length": 262,
"cds_start": 283,
"cds_end": null,
"cds_length": 789,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000334976.11",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_206538.4"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EMC10",
"gene_hgnc_id": 27609,
"hgvs_c": "c.283C>T",
"hgvs_p": "p.Arg95Trp",
"transcript": "ENST00000334976.11",
"protein_id": "ENSP00000334037.6",
"transcript_support_level": 1,
"aa_start": 95,
"aa_end": null,
"aa_length": 262,
"cds_start": 283,
"cds_end": null,
"cds_length": 789,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_206538.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000334976.11"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EMC10",
"gene_hgnc_id": 27609,
"hgvs_c": "c.283C>T",
"hgvs_p": "p.Arg95Trp",
"transcript": "ENST00000376918.7",
"protein_id": "ENSP00000366117.2",
"transcript_support_level": 1,
"aa_start": 95,
"aa_end": null,
"aa_length": 254,
"cds_start": 283,
"cds_end": null,
"cds_length": 765,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000376918.7"
},
{
"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": "EMC10",
"gene_hgnc_id": 27609,
"hgvs_c": "n.*219C>T",
"hgvs_p": null,
"transcript": "ENST00000601780.5",
"protein_id": "ENSP00000470164.1",
"transcript_support_level": 1,
"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": "nonsense_mediated_decay",
"feature": "ENST00000601780.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EMC10",
"gene_hgnc_id": 27609,
"hgvs_c": "n.*219C>T",
"hgvs_p": null,
"transcript": "ENST00000601780.5",
"protein_id": "ENSP00000470164.1",
"transcript_support_level": 1,
"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": "nonsense_mediated_decay",
"feature": "ENST00000601780.5"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EMC10",
"gene_hgnc_id": 27609,
"hgvs_c": "c.283C>T",
"hgvs_p": "p.Arg95Trp",
"transcript": "ENST00000598585.1",
"protein_id": "ENSP00000472420.1",
"transcript_support_level": 5,
"aa_start": 95,
"aa_end": null,
"aa_length": 371,
"cds_start": 283,
"cds_end": null,
"cds_length": 1116,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000598585.1"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EMC10",
"gene_hgnc_id": 27609,
"hgvs_c": "c.283C>T",
"hgvs_p": "p.Arg95Trp",
"transcript": "NM_175063.6",
"protein_id": "NP_778233.4",
"transcript_support_level": null,
"aa_start": 95,
"aa_end": null,
"aa_length": 254,
"cds_start": 283,
"cds_end": null,
"cds_length": 765,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_175063.6"
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EMC10",
"gene_hgnc_id": 27609,
"hgvs_c": "c.252C>T",
"hgvs_p": "p.Ser84Ser",
"transcript": "ENST00000597799.1",
"protein_id": "ENSP00000471764.1",
"transcript_support_level": 3,
"aa_start": 84,
"aa_end": null,
"aa_length": 87,
"cds_start": 252,
"cds_end": null,
"cds_length": 266,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000597799.1"
},
{
"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": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EMC10",
"gene_hgnc_id": 27609,
"hgvs_c": "n.*219C>T",
"hgvs_p": null,
"transcript": "ENST00000599293.1",
"protein_id": "ENSP00000472714.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000599293.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EMC10",
"gene_hgnc_id": 27609,
"hgvs_c": "n.*219C>T",
"hgvs_p": null,
"transcript": "ENST00000599293.1",
"protein_id": "ENSP00000472714.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000599293.1"
},
{
"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": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EMC10",
"gene_hgnc_id": 27609,
"hgvs_c": "c.*35C>T",
"hgvs_p": null,
"transcript": "ENST00000597426.1",
"protein_id": "ENSP00000470949.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 42,
"cds_start": null,
"cds_end": null,
"cds_length": 131,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000597426.1"
}
],
"gene_symbol": "EMC10",
"gene_hgnc_id": 27609,
"dbsnp": "rs764238587",
"frequency_reference_population": 0.0000149451325,
"hom_count_reference_population": 0,
"allele_count_reference_population": 24,
"gnomad_exomes_af": 0.0000151333,
"gnomad_genomes_af": 0.0000131473,
"gnomad_exomes_ac": 22,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.5059921145439148,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.265,
"revel_prediction": "Benign",
"alphamissense_score": 0.7613,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.14,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 3.659,
"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": 2,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "NM_206538.4",
"gene_symbol": "EMC10",
"hgnc_id": 27609,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.283C>T",
"hgvs_p": "p.Arg95Trp"
}
],
"clinvar_disease": "Inborn genetic diseases",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Inborn genetic diseases",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}