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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: 20-45840653-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=20&pos=45840653&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "20",
"pos": 45840653,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_001042633.3",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "L",
"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": "SNX21",
"gene_hgnc_id": 16154,
"hgvs_c": "c.473C>T",
"hgvs_p": "p.Pro158Leu",
"transcript": "ENST00000462307.5",
"protein_id": "ENSP00000420169.1",
"transcript_support_level": 1,
"aa_start": 158,
"aa_end": null,
"aa_length": 158,
"cds_start": 473,
"cds_end": null,
"cds_length": 477,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000462307.5"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SNX21",
"gene_hgnc_id": 16154,
"hgvs_c": "c.462C>T",
"hgvs_p": "p.Ala154Ala",
"transcript": "NM_033421.4",
"protein_id": "NP_219489.1",
"transcript_support_level": null,
"aa_start": 154,
"aa_end": null,
"aa_length": 373,
"cds_start": 462,
"cds_end": null,
"cds_length": 1122,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000491381.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_033421.4"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SNX21",
"gene_hgnc_id": 16154,
"hgvs_c": "c.462C>T",
"hgvs_p": "p.Ala154Ala",
"transcript": "ENST00000491381.6",
"protein_id": "ENSP00000418593.1",
"transcript_support_level": 1,
"aa_start": 154,
"aa_end": null,
"aa_length": 373,
"cds_start": 462,
"cds_end": null,
"cds_length": 1122,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_033421.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000491381.6"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SNX21",
"gene_hgnc_id": 16154,
"hgvs_c": "c.462C>T",
"hgvs_p": "p.Ala154Ala",
"transcript": "ENST00000342644.9",
"protein_id": "ENSP00000344586.5",
"transcript_support_level": 1,
"aa_start": 154,
"aa_end": null,
"aa_length": 199,
"cds_start": 462,
"cds_end": null,
"cds_length": 600,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000342644.9"
},
{
"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": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SNX21",
"gene_hgnc_id": 16154,
"hgvs_c": "n.566C>T",
"hgvs_p": null,
"transcript": "ENST00000372547.5",
"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": "retained_intron",
"feature": "ENST00000372547.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SNX21",
"gene_hgnc_id": 16154,
"hgvs_c": "n.781C>T",
"hgvs_p": null,
"transcript": "ENST00000472219.5",
"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": "ENST00000472219.5"
},
{
"aa_ref": "P",
"aa_alt": "L",
"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": "SNX21",
"gene_hgnc_id": 16154,
"hgvs_c": "c.473C>T",
"hgvs_p": "p.Pro158Leu",
"transcript": "NM_001042633.3",
"protein_id": "NP_001036098.1",
"transcript_support_level": null,
"aa_start": 158,
"aa_end": null,
"aa_length": 158,
"cds_start": 473,
"cds_end": null,
"cds_length": 477,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001042633.3"
},
{
"aa_ref": "P",
"aa_alt": "L",
"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": "SNX21",
"gene_hgnc_id": 16154,
"hgvs_c": "c.455C>T",
"hgvs_p": "p.Pro152Leu",
"transcript": "NM_001042632.3",
"protein_id": "NP_001036097.1",
"transcript_support_level": null,
"aa_start": 152,
"aa_end": null,
"aa_length": 152,
"cds_start": 455,
"cds_end": null,
"cds_length": 459,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001042632.3"
},
{
"aa_ref": "P",
"aa_alt": "L",
"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": "SNX21",
"gene_hgnc_id": 16154,
"hgvs_c": "c.446C>T",
"hgvs_p": "p.Pro149Leu",
"transcript": "ENST00000372541.1",
"protein_id": "ENSP00000361619.1",
"transcript_support_level": 2,
"aa_start": 149,
"aa_end": null,
"aa_length": 149,
"cds_start": 446,
"cds_end": null,
"cds_length": 450,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000372541.1"
},
{
"aa_ref": "A",
"aa_alt": "A",
"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": "SNX21",
"gene_hgnc_id": 16154,
"hgvs_c": "c.435C>T",
"hgvs_p": "p.Ala145Ala",
"transcript": "ENST00000372542.5",
"protein_id": "ENSP00000361620.1",
"transcript_support_level": 2,
"aa_start": 145,
"aa_end": null,
"aa_length": 364,
"cds_start": 435,
"cds_end": null,
"cds_length": 1095,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000372542.5"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SNX21",
"gene_hgnc_id": 16154,
"hgvs_c": "c.462C>T",
"hgvs_p": "p.Ala154Ala",
"transcript": "NM_152897.3",
"protein_id": "NP_690857.1",
"transcript_support_level": null,
"aa_start": 154,
"aa_end": null,
"aa_length": 199,
"cds_start": 462,
"cds_end": null,
"cds_length": 600,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_152897.3"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SNX21",
"gene_hgnc_id": 16154,
"hgvs_c": "c.168C>T",
"hgvs_p": "p.Ala56Ala",
"transcript": "XM_005260608.5",
"protein_id": "XP_005260665.1",
"transcript_support_level": null,
"aa_start": 56,
"aa_end": null,
"aa_length": 275,
"cds_start": 168,
"cds_end": null,
"cds_length": 828,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005260608.5"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SNX21",
"gene_hgnc_id": 16154,
"hgvs_c": "c.18C>T",
"hgvs_p": "p.Ala6Ala",
"transcript": "XM_011529095.3",
"protein_id": "XP_011527397.1",
"transcript_support_level": null,
"aa_start": 6,
"aa_end": null,
"aa_length": 225,
"cds_start": 18,
"cds_end": null,
"cds_length": 678,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011529095.3"
},
{
"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": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SNX21",
"gene_hgnc_id": 16154,
"hgvs_c": "n.484C>T",
"hgvs_p": null,
"transcript": "ENST00000344780.4",
"protein_id": null,
"transcript_support_level": 2,
"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": "ENST00000344780.4"
},
{
"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": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SNX21",
"gene_hgnc_id": 16154,
"hgvs_c": "n.236C>T",
"hgvs_p": null,
"transcript": "ENST00000465997.1",
"protein_id": null,
"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": "pseudogene",
"feature": "ENST00000465997.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SNX21",
"gene_hgnc_id": 16154,
"hgvs_c": "n.389C>T",
"hgvs_p": null,
"transcript": "ENST00000478230.5",
"protein_id": null,
"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": "pseudogene",
"feature": "ENST00000478230.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SNX21",
"gene_hgnc_id": 16154,
"hgvs_c": "n.383C>T",
"hgvs_p": null,
"transcript": "ENST00000486336.1",
"protein_id": null,
"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": "retained_intron",
"feature": "ENST00000486336.1"
}
],
"gene_symbol": "SNX21",
"gene_hgnc_id": 16154,
"dbsnp": "rs200389045",
"frequency_reference_population": 0.00003283661,
"hom_count_reference_population": 0,
"allele_count_reference_population": 53,
"gnomad_exomes_af": 0.0000328354,
"gnomad_genomes_af": 0.0000328485,
"gnomad_exomes_ac": 48,
"gnomad_genomes_ac": 5,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.16717833280563354,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.03999999910593033,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.049,
"revel_prediction": "Benign",
"alphamissense_score": 0.281,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.04,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 2.145,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.04,
"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": "Likely_benign",
"acmg_criteria": "PM2,BP4_Moderate,BP6_Moderate",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate",
"BP6_Moderate"
],
"verdict": "Likely_benign",
"transcript": "NM_001042633.3",
"gene_symbol": "SNX21",
"hgnc_id": 16154,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.473C>T",
"hgvs_p": "p.Pro158Leu"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}