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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: 5-120686024-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=120686024&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 120686024,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_001300783.2",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRR16",
"gene_hgnc_id": 29654,
"hgvs_c": "c.230C>T",
"hgvs_p": "p.Thr77Met",
"transcript": "NM_001300783.2",
"protein_id": "NP_001287712.1",
"transcript_support_level": null,
"aa_start": 77,
"aa_end": null,
"aa_length": 304,
"cds_start": 230,
"cds_end": null,
"cds_length": 915,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000407149.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001300783.2"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRR16",
"gene_hgnc_id": 29654,
"hgvs_c": "c.230C>T",
"hgvs_p": "p.Thr77Met",
"transcript": "ENST00000407149.7",
"protein_id": "ENSP00000385118.2",
"transcript_support_level": 1,
"aa_start": 77,
"aa_end": null,
"aa_length": 304,
"cds_start": 230,
"cds_end": null,
"cds_length": 915,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001300783.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000407149.7"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRR16",
"gene_hgnc_id": 29654,
"hgvs_c": "c.161C>T",
"hgvs_p": "p.Thr54Met",
"transcript": "ENST00000379551.2",
"protein_id": "ENSP00000368869.2",
"transcript_support_level": 1,
"aa_start": 54,
"aa_end": null,
"aa_length": 281,
"cds_start": 161,
"cds_end": null,
"cds_length": 846,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000379551.2"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRR16",
"gene_hgnc_id": 29654,
"hgvs_c": "c.71C>T",
"hgvs_p": "p.Thr24Met",
"transcript": "ENST00000446965.2",
"protein_id": "ENSP00000405491.2",
"transcript_support_level": 1,
"aa_start": 24,
"aa_end": null,
"aa_length": 251,
"cds_start": 71,
"cds_end": null,
"cds_length": 756,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000446965.2"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRR16",
"gene_hgnc_id": 29654,
"hgvs_c": "c.161C>T",
"hgvs_p": "p.Thr54Met",
"transcript": "NM_016644.3",
"protein_id": "NP_057728.1",
"transcript_support_level": null,
"aa_start": 54,
"aa_end": null,
"aa_length": 281,
"cds_start": 161,
"cds_end": null,
"cds_length": 846,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_016644.3"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRR16",
"gene_hgnc_id": 29654,
"hgvs_c": "c.20C>T",
"hgvs_p": "p.Thr7Met",
"transcript": "NM_001308087.2",
"protein_id": "NP_001295016.1",
"transcript_support_level": null,
"aa_start": 7,
"aa_end": null,
"aa_length": 234,
"cds_start": 20,
"cds_end": null,
"cds_length": 705,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001308087.2"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRR16",
"gene_hgnc_id": 29654,
"hgvs_c": "c.20C>T",
"hgvs_p": "p.Thr7Met",
"transcript": "NM_001308088.1",
"protein_id": "NP_001295017.1",
"transcript_support_level": null,
"aa_start": 7,
"aa_end": null,
"aa_length": 234,
"cds_start": 20,
"cds_end": null,
"cds_length": 705,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001308088.1"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRR16",
"gene_hgnc_id": 29654,
"hgvs_c": "c.20C>T",
"hgvs_p": "p.Thr7Met",
"transcript": "ENST00000505123.5",
"protein_id": "ENSP00000423446.1",
"transcript_support_level": 3,
"aa_start": 7,
"aa_end": null,
"aa_length": 234,
"cds_start": 20,
"cds_end": null,
"cds_length": 705,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000505123.5"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRR16",
"gene_hgnc_id": 29654,
"hgvs_c": "c.20C>T",
"hgvs_p": "p.Thr7Met",
"transcript": "ENST00000509923.1",
"protein_id": "ENSP00000421256.1",
"transcript_support_level": 3,
"aa_start": 7,
"aa_end": null,
"aa_length": 141,
"cds_start": 20,
"cds_end": null,
"cds_length": 427,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000509923.1"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRR16",
"gene_hgnc_id": 29654,
"hgvs_c": "c.230C>T",
"hgvs_p": "p.Thr77Met",
"transcript": "XM_047417289.1",
"protein_id": "XP_047273245.1",
"transcript_support_level": null,
"aa_start": 77,
"aa_end": null,
"aa_length": 304,
"cds_start": 230,
"cds_end": null,
"cds_length": 915,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047417289.1"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRR16",
"gene_hgnc_id": 29654,
"hgvs_c": "c.83C>T",
"hgvs_p": "p.Thr28Met",
"transcript": "XM_011543452.3",
"protein_id": "XP_011541754.1",
"transcript_support_level": null,
"aa_start": 28,
"aa_end": null,
"aa_length": 255,
"cds_start": 83,
"cds_end": null,
"cds_length": 768,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011543452.3"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRR16",
"gene_hgnc_id": 29654,
"hgvs_c": "c.20C>T",
"hgvs_p": "p.Thr7Met",
"transcript": "XM_047417290.1",
"protein_id": "XP_047273246.1",
"transcript_support_level": null,
"aa_start": 7,
"aa_end": null,
"aa_length": 234,
"cds_start": 20,
"cds_end": null,
"cds_length": 705,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047417290.1"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRR16",
"gene_hgnc_id": 29654,
"hgvs_c": "c.20C>T",
"hgvs_p": "p.Thr7Met",
"transcript": "XM_047417291.1",
"protein_id": "XP_047273247.1",
"transcript_support_level": null,
"aa_start": 7,
"aa_end": null,
"aa_length": 234,
"cds_start": 20,
"cds_end": null,
"cds_length": 705,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047417291.1"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRR16",
"gene_hgnc_id": 29654,
"hgvs_c": "c.20C>T",
"hgvs_p": "p.Thr7Met",
"transcript": "XM_047417292.1",
"protein_id": "XP_047273248.1",
"transcript_support_level": null,
"aa_start": 7,
"aa_end": null,
"aa_length": 234,
"cds_start": 20,
"cds_end": null,
"cds_length": 705,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047417292.1"
}
],
"gene_symbol": "PRR16",
"gene_hgnc_id": 29654,
"dbsnp": "rs759341558",
"frequency_reference_population": 0.000026641652,
"hom_count_reference_population": 0,
"allele_count_reference_population": 43,
"gnomad_exomes_af": 0.0000266791,
"gnomad_genomes_af": 0.0000262822,
"gnomad_exomes_ac": 39,
"gnomad_genomes_ac": 4,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.5022919774055481,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.408,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.3868,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.06,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 7.542,
"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": 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_001300783.2",
"gene_symbol": "PRR16",
"hgnc_id": 29654,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.230C>T",
"hgvs_p": "p.Thr77Met"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}