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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: 3-58310575-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=58310575&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 58310575,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_007042.6",
"consequences": [
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPP14",
"gene_hgnc_id": 30327,
"hgvs_c": "c.146A>G",
"hgvs_p": "p.Lys49Arg",
"transcript": "NM_007042.6",
"protein_id": "NP_008973.1",
"transcript_support_level": null,
"aa_start": 49,
"aa_end": null,
"aa_length": 124,
"cds_start": 146,
"cds_end": null,
"cds_length": 375,
"cdna_start": 340,
"cdna_end": null,
"cdna_length": 3266,
"mane_select": "ENST00000295959.10",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_007042.6"
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPP14",
"gene_hgnc_id": 30327,
"hgvs_c": "c.146A>G",
"hgvs_p": "p.Lys49Arg",
"transcript": "ENST00000295959.10",
"protein_id": "ENSP00000295959.5",
"transcript_support_level": 1,
"aa_start": 49,
"aa_end": null,
"aa_length": 124,
"cds_start": 146,
"cds_end": null,
"cds_length": 375,
"cdna_start": 340,
"cdna_end": null,
"cdna_length": 3266,
"mane_select": "NM_007042.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000295959.10"
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPP14",
"gene_hgnc_id": 30327,
"hgvs_c": "c.146A>G",
"hgvs_p": "p.Lys49Arg",
"transcript": "ENST00000445193.7",
"protein_id": "ENSP00000412894.2",
"transcript_support_level": 1,
"aa_start": 49,
"aa_end": null,
"aa_length": 124,
"cds_start": 146,
"cds_end": null,
"cds_length": 375,
"cdna_start": 557,
"cdna_end": null,
"cdna_length": 7985,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000445193.7"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HTD2",
"gene_hgnc_id": 53111,
"hgvs_c": "c.-347A>G",
"hgvs_p": null,
"transcript": "NM_001348712.2",
"protein_id": "NP_001335641.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 168,
"cds_start": null,
"cds_end": null,
"cds_length": 507,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3127,
"mane_select": "ENST00000461393.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001348712.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HTD2",
"gene_hgnc_id": 53111,
"hgvs_c": "c.-347A>G",
"hgvs_p": null,
"transcript": "ENST00000461393.7",
"protein_id": "ENSP00000484277.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 168,
"cds_start": null,
"cds_end": null,
"cds_length": 507,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3127,
"mane_select": "NM_001348712.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000461393.7"
},
{
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPP14",
"gene_hgnc_id": 30327,
"hgvs_c": "n.422A>G",
"hgvs_p": null,
"transcript": "ENST00000463550.2",
"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": 658,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000463550.2"
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPP14",
"gene_hgnc_id": 30327,
"hgvs_c": "c.146A>G",
"hgvs_p": "p.Lys49Arg",
"transcript": "NM_001098783.3",
"protein_id": "NP_001092253.1",
"transcript_support_level": null,
"aa_start": 49,
"aa_end": null,
"aa_length": 124,
"cds_start": 146,
"cds_end": null,
"cds_length": 375,
"cdna_start": 299,
"cdna_end": null,
"cdna_length": 3225,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001098783.3"
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPP14",
"gene_hgnc_id": 30327,
"hgvs_c": "c.146A>G",
"hgvs_p": "p.Lys49Arg",
"transcript": "ENST00000466547.1",
"protein_id": "ENSP00000419909.1",
"transcript_support_level": 3,
"aa_start": 49,
"aa_end": null,
"aa_length": 124,
"cds_start": 146,
"cds_end": null,
"cds_length": 375,
"cdna_start": 294,
"cdna_end": null,
"cdna_length": 805,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000466547.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HTD2",
"gene_hgnc_id": 53111,
"hgvs_c": "c.-445A>G",
"hgvs_p": null,
"transcript": "NM_001348713.1",
"protein_id": "NP_001335642.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 168,
"cds_start": null,
"cds_end": null,
"cds_length": 507,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3266,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001348713.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HTD2",
"gene_hgnc_id": 53111,
"hgvs_c": "c.-347A>G",
"hgvs_p": null,
"transcript": "NM_001348714.1",
"protein_id": "NP_001335643.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 168,
"cds_start": null,
"cds_end": null,
"cds_length": 507,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3168,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001348714.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HTD2",
"gene_hgnc_id": 53111,
"hgvs_c": "c.-446A>G",
"hgvs_p": null,
"transcript": "ENST00000477305.5",
"protein_id": "ENSP00000481593.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 168,
"cds_start": null,
"cds_end": null,
"cds_length": 507,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1531,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000477305.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HTD2",
"gene_hgnc_id": 53111,
"hgvs_c": "c.-347A>G",
"hgvs_p": null,
"transcript": "ENST00000481972.5",
"protein_id": "ENSP00000482940.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 168,
"cds_start": null,
"cds_end": null,
"cds_length": 507,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1378,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000481972.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HTD2",
"gene_hgnc_id": 53111,
"hgvs_c": "c.-445A>G",
"hgvs_p": null,
"transcript": "ENST00000474660.5",
"protein_id": "ENSP00000477762.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 75,
"cds_start": null,
"cds_end": null,
"cds_length": 229,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 888,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000474660.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HTD2",
"gene_hgnc_id": 53111,
"hgvs_c": "c.-347A>G",
"hgvs_p": null,
"transcript": "ENST00000476007.2",
"protein_id": "ENSP00000478964.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 70,
"cds_start": null,
"cds_end": null,
"cds_length": 215,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 847,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000476007.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "HTD2",
"gene_hgnc_id": 53111,
"hgvs_c": "c.-331+4158A>G",
"hgvs_p": null,
"transcript": "NM_001348715.1",
"protein_id": "NP_001335644.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 168,
"cds_start": null,
"cds_end": null,
"cds_length": 507,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3083,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001348715.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "HTD2",
"gene_hgnc_id": 53111,
"hgvs_c": "c.-331+4158A>G",
"hgvs_p": null,
"transcript": "ENST00000475412.5",
"protein_id": "ENSP00000481678.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 53,
"cds_start": null,
"cds_end": null,
"cds_length": 162,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 648,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000475412.5"
},
{
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPP14",
"gene_hgnc_id": 30327,
"hgvs_c": "n.338A>G",
"hgvs_p": null,
"transcript": "ENST00000461797.5",
"protein_id": null,
"transcript_support_level": 4,
"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": 531,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000461797.5"
},
{
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HTD2",
"gene_hgnc_id": 53111,
"hgvs_c": "n.356A>G",
"hgvs_p": null,
"transcript": "ENST00000498618.5",
"protein_id": null,
"transcript_support_level": 4,
"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": 557,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000498618.5"
}
],
"gene_symbol": "RPP14",
"gene_hgnc_id": 30327,
"dbsnp": "rs962925304",
"frequency_reference_population": 0.0000055799214,
"hom_count_reference_population": 0,
"allele_count_reference_population": 9,
"gnomad_exomes_af": 0.00000547654,
"gnomad_genomes_af": 0.00000657246,
"gnomad_exomes_ac": 8,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.13859587907791138,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.05000000074505806,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.062,
"revel_prediction": "Benign",
"alphamissense_score": 0.0699,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.52,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 3.022,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.05,
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_007042.6",
"gene_symbol": "RPP14",
"hgnc_id": 30327,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.146A>G",
"hgvs_p": "p.Lys49Arg"
},
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_001348712.2",
"gene_symbol": "HTD2",
"hgnc_id": 53111,
"effects": [
"5_prime_UTR_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.-347A>G",
"hgvs_p": null
}
],
"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
}