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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: 5-80873118-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=80873118&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 80873118,
"ref": "G",
"alt": "A",
"effect": "missense_variant,splice_region_variant",
"transcript": "ENST00000265081.7",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH3",
"gene_hgnc_id": 7326,
"hgvs_c": "c.3133G>A",
"hgvs_p": "p.Ala1045Thr",
"transcript": "NM_002439.5",
"protein_id": "NP_002430.3",
"transcript_support_level": null,
"aa_start": 1045,
"aa_end": null,
"aa_length": 1137,
"cds_start": 3133,
"cds_end": null,
"cds_length": 3414,
"cdna_start": 3209,
"cdna_end": null,
"cdna_length": 4443,
"mane_select": "ENST00000265081.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH3",
"gene_hgnc_id": 7326,
"hgvs_c": "c.3133G>A",
"hgvs_p": "p.Ala1045Thr",
"transcript": "ENST00000265081.7",
"protein_id": "ENSP00000265081.6",
"transcript_support_level": 1,
"aa_start": 1045,
"aa_end": null,
"aa_length": 1137,
"cds_start": 3133,
"cds_end": null,
"cds_length": 3414,
"cdna_start": 3209,
"cdna_end": null,
"cdna_length": 4443,
"mane_select": "NM_002439.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH3",
"gene_hgnc_id": 7326,
"hgvs_c": "c.2965G>A",
"hgvs_p": "p.Ala989Thr",
"transcript": "ENST00000658259.1",
"protein_id": "ENSP00000499617.1",
"transcript_support_level": null,
"aa_start": 989,
"aa_end": null,
"aa_length": 1081,
"cds_start": 2965,
"cds_end": null,
"cds_length": 3246,
"cdna_start": 3007,
"cdna_end": null,
"cdna_length": 3295,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH3",
"gene_hgnc_id": 7326,
"hgvs_c": "c.2938G>A",
"hgvs_p": "p.Ala980Thr",
"transcript": "ENST00000667069.1",
"protein_id": "ENSP00000499502.1",
"transcript_support_level": null,
"aa_start": 980,
"aa_end": null,
"aa_length": 1072,
"cds_start": 2938,
"cds_end": null,
"cds_length": 3219,
"cdna_start": 2972,
"cdna_end": null,
"cdna_length": 3964,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH3",
"gene_hgnc_id": 7326,
"hgvs_c": "n.*457G>A",
"hgvs_p": null,
"transcript": "ENST00000670357.1",
"protein_id": "ENSP00000499791.1",
"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": 4486,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH3",
"gene_hgnc_id": 7326,
"hgvs_c": "n.*457G>A",
"hgvs_p": null,
"transcript": "ENST00000670357.1",
"protein_id": "ENSP00000499791.1",
"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": 4486,
"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",
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH3",
"gene_hgnc_id": 7326,
"hgvs_c": "n.*375G>A",
"hgvs_p": null,
"transcript": "ENST00000659302.1",
"protein_id": "ENSP00000499680.1",
"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": 1570,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH3",
"gene_hgnc_id": 7326,
"hgvs_c": "n.*375G>A",
"hgvs_p": null,
"transcript": "ENST00000659302.1",
"protein_id": "ENSP00000499680.1",
"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": 1570,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "MSH3",
"gene_hgnc_id": 7326,
"dbsnp": "rs26279",
"frequency_reference_population": 0.717394,
"hom_count_reference_population": 415407,
"allele_count_reference_population": 1155132,
"gnomad_exomes_af": 0.718588,
"gnomad_genomes_af": 0.705945,
"gnomad_exomes_ac": 1047769,
"gnomad_genomes_ac": 107363,
"gnomad_exomes_homalt": 377500,
"gnomad_genomes_homalt": 37907,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 8.821012897897162e-7,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.108,
"revel_prediction": "Benign",
"alphamissense_score": 0.0661,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.51,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.922,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.02,
"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": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BA1",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000265081.7",
"gene_symbol": "MSH3",
"hgnc_id": 7326,
"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.3133G>A",
"hgvs_p": "p.Ala1045Thr"
}
],
"clinvar_disease": "Hereditary cancer-predisposing syndrome,not provided",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:5",
"phenotype_combined": "Hereditary cancer-predisposing syndrome|not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}