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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: 5-80854162-A-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=80854162&ref=A&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 80854162,
"ref": "A",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_002439.5",
"consequences": [
{
"aa_ref": "Q",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH3",
"gene_hgnc_id": 7326,
"hgvs_c": "c.2846A>T",
"hgvs_p": "p.Gln949Leu",
"transcript": "NM_002439.5",
"protein_id": "NP_002430.3",
"transcript_support_level": null,
"aa_start": 949,
"aa_end": null,
"aa_length": 1137,
"cds_start": 2846,
"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": "Q",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH3",
"gene_hgnc_id": 7326,
"hgvs_c": "c.2846A>T",
"hgvs_p": "p.Gln949Leu",
"transcript": "ENST00000265081.7",
"protein_id": "ENSP00000265081.6",
"transcript_support_level": 1,
"aa_start": 949,
"aa_end": null,
"aa_length": 1137,
"cds_start": 2846,
"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": "Q",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH3",
"gene_hgnc_id": 7326,
"hgvs_c": "c.2678A>T",
"hgvs_p": "p.Gln893Leu",
"transcript": "ENST00000658259.1",
"protein_id": "ENSP00000499617.1",
"transcript_support_level": null,
"aa_start": 893,
"aa_end": null,
"aa_length": 1081,
"cds_start": 2678,
"cds_end": null,
"cds_length": 3246,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000658259.1"
},
{
"aa_ref": "Q",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH3",
"gene_hgnc_id": 7326,
"hgvs_c": "c.2651A>T",
"hgvs_p": "p.Gln884Leu",
"transcript": "ENST00000667069.1",
"protein_id": "ENSP00000499502.1",
"transcript_support_level": null,
"aa_start": 884,
"aa_end": null,
"aa_length": 1072,
"cds_start": 2651,
"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": true,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH3",
"gene_hgnc_id": 7326,
"hgvs_c": "n.*170A>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": [
"3_prime_UTR_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH3",
"gene_hgnc_id": 7326,
"hgvs_c": "n.*170A>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": "Q",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH3",
"gene_hgnc_id": 7326,
"hgvs_c": "c.2846A>T",
"hgvs_p": "p.Gln949Leu",
"transcript": "ENST00000875834.1",
"protein_id": "ENSP00000545893.1",
"transcript_support_level": null,
"aa_start": 949,
"aa_end": null,
"aa_length": 1158,
"cds_start": 2846,
"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": "Q",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH3",
"gene_hgnc_id": 7326,
"hgvs_c": "c.2750A>T",
"hgvs_p": "p.Gln917Leu",
"transcript": "ENST00000969134.1",
"protein_id": "ENSP00000639193.1",
"transcript_support_level": null,
"aa_start": 917,
"aa_end": null,
"aa_length": 1105,
"cds_start": 2750,
"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": "Q",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH3",
"gene_hgnc_id": 7326,
"hgvs_c": "c.2603A>T",
"hgvs_p": "p.Gln868Leu",
"transcript": "ENST00000875835.1",
"protein_id": "ENSP00000545894.1",
"transcript_support_level": null,
"aa_start": 868,
"aa_end": null,
"aa_length": 1056,
"cds_start": 2603,
"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": "Q",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH3",
"gene_hgnc_id": 7326,
"hgvs_c": "c.2534A>T",
"hgvs_p": "p.Gln845Leu",
"transcript": "ENST00000933917.1",
"protein_id": "ENSP00000603976.1",
"transcript_support_level": null,
"aa_start": 845,
"aa_end": null,
"aa_length": 1033,
"cds_start": 2534,
"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": "Q",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH3",
"gene_hgnc_id": 7326,
"hgvs_c": "c.2087A>T",
"hgvs_p": "p.Gln696Leu",
"transcript": "ENST00000875836.1",
"protein_id": "ENSP00000545895.1",
"transcript_support_level": null,
"aa_start": 696,
"aa_end": null,
"aa_length": 884,
"cds_start": 2087,
"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": "Q",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH3",
"gene_hgnc_id": 7326,
"hgvs_c": "c.1874A>T",
"hgvs_p": "p.Gln625Leu",
"transcript": "ENST00000969133.1",
"protein_id": "ENSP00000639192.1",
"transcript_support_level": null,
"aa_start": 625,
"aa_end": null,
"aa_length": 813,
"cds_start": 1874,
"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": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH3",
"gene_hgnc_id": 7326,
"hgvs_c": "n.*88A>T",
"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": 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": "ENST00000659302.1"
},
{
"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": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH3",
"gene_hgnc_id": 7326,
"hgvs_c": "n.*88A>T",
"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": 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": "ENST00000659302.1"
}
],
"gene_symbol": "MSH3",
"gene_hgnc_id": 7326,
"dbsnp": "rs184967",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": 0,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 0,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.5518733263015747,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.357,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.2123,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.23,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.429,
"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_002439.5",
"gene_symbol": "MSH3",
"hgnc_id": 7326,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.2846A>T",
"hgvs_p": "p.Gln949Leu"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}