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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: 1-154925143-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=154925143&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 154925143,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_006556.4",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMVK",
"gene_hgnc_id": 9141,
"hgvs_c": "c.565C>T",
"hgvs_p": "p.Arg189Cys",
"transcript": "NM_006556.4",
"protein_id": "NP_006547.1",
"transcript_support_level": null,
"aa_start": 189,
"aa_end": null,
"aa_length": 192,
"cds_start": 565,
"cds_end": null,
"cds_length": 579,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000368467.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_006556.4"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMVK",
"gene_hgnc_id": 9141,
"hgvs_c": "c.565C>T",
"hgvs_p": "p.Arg189Cys",
"transcript": "ENST00000368467.4",
"protein_id": "ENSP00000357452.3",
"transcript_support_level": 1,
"aa_start": 189,
"aa_end": null,
"aa_length": 192,
"cds_start": 565,
"cds_end": null,
"cds_length": 579,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_006556.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000368467.4"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMVK",
"gene_hgnc_id": 9141,
"hgvs_c": "c.757C>T",
"hgvs_p": "p.Arg253Cys",
"transcript": "ENST00000940351.1",
"protein_id": "ENSP00000610410.1",
"transcript_support_level": null,
"aa_start": 253,
"aa_end": null,
"aa_length": 256,
"cds_start": 757,
"cds_end": null,
"cds_length": 771,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000940351.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMVK",
"gene_hgnc_id": 9141,
"hgvs_c": "c.604C>T",
"hgvs_p": "p.Arg202Cys",
"transcript": "ENST00000885059.1",
"protein_id": "ENSP00000555118.1",
"transcript_support_level": null,
"aa_start": 202,
"aa_end": null,
"aa_length": 205,
"cds_start": 604,
"cds_end": null,
"cds_length": 618,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000885059.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMVK",
"gene_hgnc_id": 9141,
"hgvs_c": "c.571C>T",
"hgvs_p": "p.Arg191Cys",
"transcript": "ENST00000940350.1",
"protein_id": "ENSP00000610409.1",
"transcript_support_level": null,
"aa_start": 191,
"aa_end": null,
"aa_length": 194,
"cds_start": 571,
"cds_end": null,
"cds_length": 585,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000940350.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMVK",
"gene_hgnc_id": 9141,
"hgvs_c": "c.562C>T",
"hgvs_p": "p.Arg188Cys",
"transcript": "ENST00000885057.1",
"protein_id": "ENSP00000555116.1",
"transcript_support_level": null,
"aa_start": 188,
"aa_end": null,
"aa_length": 191,
"cds_start": 562,
"cds_end": null,
"cds_length": 576,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000885057.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMVK",
"gene_hgnc_id": 9141,
"hgvs_c": "c.544C>T",
"hgvs_p": "p.Arg182Cys",
"transcript": "ENST00000885055.1",
"protein_id": "ENSP00000555114.1",
"transcript_support_level": null,
"aa_start": 182,
"aa_end": null,
"aa_length": 185,
"cds_start": 544,
"cds_end": null,
"cds_length": 558,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000885055.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMVK",
"gene_hgnc_id": 9141,
"hgvs_c": "c.523C>T",
"hgvs_p": "p.Arg175Cys",
"transcript": "NM_001323011.3",
"protein_id": "NP_001309940.1",
"transcript_support_level": null,
"aa_start": 175,
"aa_end": null,
"aa_length": 178,
"cds_start": 523,
"cds_end": null,
"cds_length": 537,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001323011.3"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMVK",
"gene_hgnc_id": 9141,
"hgvs_c": "c.442C>T",
"hgvs_p": "p.Arg148Cys",
"transcript": "ENST00000885058.1",
"protein_id": "ENSP00000555117.1",
"transcript_support_level": null,
"aa_start": 148,
"aa_end": null,
"aa_length": 151,
"cds_start": 442,
"cds_end": null,
"cds_length": 456,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000885058.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMVK",
"gene_hgnc_id": 9141,
"hgvs_c": "c.412C>T",
"hgvs_p": "p.Arg138Cys",
"transcript": "ENST00000885056.1",
"protein_id": "ENSP00000555115.1",
"transcript_support_level": null,
"aa_start": 138,
"aa_end": null,
"aa_length": 141,
"cds_start": 412,
"cds_end": null,
"cds_length": 426,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000885056.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMVK",
"gene_hgnc_id": 9141,
"hgvs_c": "c.340C>T",
"hgvs_p": "p.Arg114Cys",
"transcript": "NM_001323012.3",
"protein_id": "NP_001309941.1",
"transcript_support_level": null,
"aa_start": 114,
"aa_end": null,
"aa_length": 117,
"cds_start": 340,
"cds_end": null,
"cds_length": 354,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001323012.3"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMVK",
"gene_hgnc_id": 9141,
"hgvs_c": "c.340C>T",
"hgvs_p": "p.Arg114Cys",
"transcript": "NM_001348696.2",
"protein_id": "NP_001335625.1",
"transcript_support_level": null,
"aa_start": 114,
"aa_end": null,
"aa_length": 117,
"cds_start": 340,
"cds_end": null,
"cds_length": 354,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001348696.2"
}
],
"gene_symbol": "PMVK",
"gene_hgnc_id": 9141,
"dbsnp": "rs370067596",
"frequency_reference_population": 0.00011538075,
"hom_count_reference_population": 0,
"allele_count_reference_population": 186,
"gnomad_exomes_af": 0.000119777,
"gnomad_genomes_af": 0.0000728467,
"gnomad_exomes_ac": 175,
"gnomad_genomes_ac": 11,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.15088483691215515,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.022,
"revel_prediction": "Benign",
"alphamissense_score": 0.0778,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.51,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.589,
"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": "Likely_benign",
"acmg_criteria": "BP4_Moderate",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 2,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate"
],
"verdict": "Likely_benign",
"transcript": "NM_006556.4",
"gene_symbol": "PMVK",
"hgnc_id": 9141,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.565C>T",
"hgvs_p": "p.Arg189Cys"
}
],
"clinvar_disease": "Inborn genetic diseases",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Inborn genetic diseases",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}