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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: 5-80654686-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=80654686&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 80654686,
"ref": "C",
"alt": "T",
"effect": "5_prime_UTR_variant",
"transcript": "NM_002439.5",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH3",
"gene_hgnc_id": 7326,
"hgvs_c": "c.-42C>T",
"hgvs_p": null,
"transcript": "NM_002439.5",
"protein_id": "NP_002430.3",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1137,
"cds_start": null,
"cds_end": null,
"cds_length": 3414,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000265081.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_002439.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH3",
"gene_hgnc_id": 7326,
"hgvs_c": "c.-42C>T",
"hgvs_p": null,
"transcript": "ENST00000265081.7",
"protein_id": "ENSP00000265081.6",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 1137,
"cds_start": null,
"cds_end": null,
"cds_length": 3414,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_002439.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000265081.7"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DHFR",
"gene_hgnc_id": 2861,
"hgvs_c": "c.-197G>A",
"hgvs_p": null,
"transcript": "NM_000791.4",
"protein_id": "NP_000782.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 187,
"cds_start": null,
"cds_end": null,
"cds_length": 564,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000439211.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_000791.4"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DHFR",
"gene_hgnc_id": 2861,
"hgvs_c": "c.-197G>A",
"hgvs_p": null,
"transcript": "ENST00000439211.7",
"protein_id": "ENSP00000396308.2",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 187,
"cds_start": null,
"cds_end": null,
"cds_length": 564,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_000791.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000439211.7"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH3",
"gene_hgnc_id": 7326,
"hgvs_c": "n.-42C>T",
"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": 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": "ENST00000670357.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH3",
"gene_hgnc_id": 7326,
"hgvs_c": "n.-42C>T",
"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": 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": "ENST00000670357.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH3",
"gene_hgnc_id": 7326,
"hgvs_c": "c.-42C>T",
"hgvs_p": null,
"transcript": "ENST00000875834.1",
"protein_id": "ENSP00000545893.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1158,
"cds_start": null,
"cds_end": null,
"cds_length": 3477,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000875834.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH3",
"gene_hgnc_id": 7326,
"hgvs_c": "c.-42C>T",
"hgvs_p": null,
"transcript": "ENST00000969134.1",
"protein_id": "ENSP00000639193.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1105,
"cds_start": null,
"cds_end": null,
"cds_length": 3318,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000969134.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH3",
"gene_hgnc_id": 7326,
"hgvs_c": "c.-42C>T",
"hgvs_p": null,
"transcript": "ENST00000933917.1",
"protein_id": "ENSP00000603976.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1033,
"cds_start": null,
"cds_end": null,
"cds_length": 3102,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000933917.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH3",
"gene_hgnc_id": 7326,
"hgvs_c": "c.-42C>T",
"hgvs_p": null,
"transcript": "ENST00000875836.1",
"protein_id": "ENSP00000545895.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 884,
"cds_start": null,
"cds_end": null,
"cds_length": 2655,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000875836.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH3",
"gene_hgnc_id": 7326,
"hgvs_c": "c.-42C>T",
"hgvs_p": null,
"transcript": "ENST00000969133.1",
"protein_id": "ENSP00000639192.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 813,
"cds_start": null,
"cds_end": null,
"cds_length": 2442,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000969133.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DHFR",
"gene_hgnc_id": 2861,
"hgvs_c": "c.-303G>A",
"hgvs_p": null,
"transcript": "NM_001290354.2",
"protein_id": "NP_001277283.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 135,
"cds_start": null,
"cds_end": null,
"cds_length": 408,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001290354.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DHFR",
"gene_hgnc_id": 2861,
"hgvs_c": "c.-197G>A",
"hgvs_p": null,
"transcript": "NM_001290357.2",
"protein_id": "NP_001277286.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 129,
"cds_start": null,
"cds_end": null,
"cds_length": 390,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001290357.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DHFR",
"gene_hgnc_id": 2861,
"hgvs_c": "n.298G>A",
"hgvs_p": null,
"transcript": "NR_110936.2",
"protein_id": null,
"transcript_support_level": null,
"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": "pseudogene",
"feature": "NR_110936.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH3",
"gene_hgnc_id": 7326,
"hgvs_c": "c.-42C>T",
"hgvs_p": null,
"transcript": "ENST00000667069.1",
"protein_id": "ENSP00000499502.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1072,
"cds_start": null,
"cds_end": null,
"cds_length": 3219,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000667069.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DHFR",
"gene_hgnc_id": 2861,
"hgvs_c": "n.-139G>A",
"hgvs_p": null,
"transcript": "ENST00000513048.5",
"protein_id": null,
"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": "pseudogene",
"feature": "ENST00000513048.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH3",
"gene_hgnc_id": 7326,
"hgvs_c": "c.-42C>T",
"hgvs_p": null,
"transcript": "ENST00000875835.1",
"protein_id": "ENSP00000545894.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1056,
"cds_start": null,
"cds_end": null,
"cds_length": 3171,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000875835.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DHFR",
"gene_hgnc_id": 2861,
"hgvs_c": "c.-197G>A",
"hgvs_p": null,
"transcript": "ENST00000505337.5",
"protein_id": "ENSP00000426474.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 187,
"cds_start": null,
"cds_end": null,
"cds_length": 564,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000505337.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DHFR",
"gene_hgnc_id": 2861,
"hgvs_c": "c.-197G>A",
"hgvs_p": null,
"transcript": "ENST00000935289.1",
"protein_id": "ENSP00000605348.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 187,
"cds_start": null,
"cds_end": null,
"cds_length": 564,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000935289.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DHFR",
"gene_hgnc_id": 2861,
"hgvs_c": "c.-303G>A",
"hgvs_p": null,
"transcript": "ENST00000504396.1",
"protein_id": "ENSP00000421334.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 135,
"cds_start": null,
"cds_end": null,
"cds_length": 408,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000504396.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DHFR",
"gene_hgnc_id": 2861,
"hgvs_c": "c.-197G>A",
"hgvs_p": null,
"transcript": "ENST00000511032.5",
"protein_id": "ENSP00000422732.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 129,
"cds_start": null,
"cds_end": null,
"cds_length": 390,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000511032.5"
}
],
"gene_symbol": "MSH3",
"gene_hgnc_id": 7326,
"dbsnp": "rs534679562",
"frequency_reference_population": 0.0004853152,
"hom_count_reference_population": 8,
"allele_count_reference_population": 755,
"gnomad_exomes_af": 0.000501428,
"gnomad_genomes_af": 0.00033619,
"gnomad_exomes_ac": 704,
"gnomad_genomes_ac": 51,
"gnomad_exomes_homalt": 8,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.7699999809265137,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.77,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.058,
"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": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BS1,BS2",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_002439.5",
"gene_symbol": "MSH3",
"hgnc_id": 7326,
"effects": [
"5_prime_UTR_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.-42C>T",
"hgvs_p": null
},
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_000791.4",
"gene_symbol": "DHFR",
"hgnc_id": 2861,
"effects": [
"5_prime_UTR_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.-197G>A",
"hgvs_p": null
}
],
"clinvar_disease": "not provided,not specified",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:1 B:1",
"phenotype_combined": "not provided|not specified",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}