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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: 1-154925209-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=154925209&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 154925209,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_006556.4",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "I",
"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.499G>A",
"hgvs_p": "p.Val167Ile",
"transcript": "NM_006556.4",
"protein_id": "NP_006547.1",
"transcript_support_level": null,
"aa_start": 167,
"aa_end": null,
"aa_length": 192,
"cds_start": 499,
"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": "V",
"aa_alt": "I",
"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.499G>A",
"hgvs_p": "p.Val167Ile",
"transcript": "ENST00000368467.4",
"protein_id": "ENSP00000357452.3",
"transcript_support_level": 1,
"aa_start": 167,
"aa_end": null,
"aa_length": 192,
"cds_start": 499,
"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": "V",
"aa_alt": "I",
"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.691G>A",
"hgvs_p": "p.Val231Ile",
"transcript": "ENST00000940351.1",
"protein_id": "ENSP00000610410.1",
"transcript_support_level": null,
"aa_start": 231,
"aa_end": null,
"aa_length": 256,
"cds_start": 691,
"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": "V",
"aa_alt": "I",
"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.538G>A",
"hgvs_p": "p.Val180Ile",
"transcript": "ENST00000885059.1",
"protein_id": "ENSP00000555118.1",
"transcript_support_level": null,
"aa_start": 180,
"aa_end": null,
"aa_length": 205,
"cds_start": 538,
"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": "V",
"aa_alt": "I",
"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.505G>A",
"hgvs_p": "p.Val169Ile",
"transcript": "ENST00000940350.1",
"protein_id": "ENSP00000610409.1",
"transcript_support_level": null,
"aa_start": 169,
"aa_end": null,
"aa_length": 194,
"cds_start": 505,
"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": "V",
"aa_alt": "I",
"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.496G>A",
"hgvs_p": "p.Val166Ile",
"transcript": "ENST00000885057.1",
"protein_id": "ENSP00000555116.1",
"transcript_support_level": null,
"aa_start": 166,
"aa_end": null,
"aa_length": 191,
"cds_start": 496,
"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": "V",
"aa_alt": "I",
"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.478G>A",
"hgvs_p": "p.Val160Ile",
"transcript": "ENST00000885055.1",
"protein_id": "ENSP00000555114.1",
"transcript_support_level": null,
"aa_start": 160,
"aa_end": null,
"aa_length": 185,
"cds_start": 478,
"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": "V",
"aa_alt": "I",
"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.457G>A",
"hgvs_p": "p.Val153Ile",
"transcript": "NM_001323011.3",
"protein_id": "NP_001309940.1",
"transcript_support_level": null,
"aa_start": 153,
"aa_end": null,
"aa_length": 178,
"cds_start": 457,
"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": "V",
"aa_alt": "I",
"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.376G>A",
"hgvs_p": "p.Val126Ile",
"transcript": "ENST00000885058.1",
"protein_id": "ENSP00000555117.1",
"transcript_support_level": null,
"aa_start": 126,
"aa_end": null,
"aa_length": 151,
"cds_start": 376,
"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": "V",
"aa_alt": "I",
"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.346G>A",
"hgvs_p": "p.Val116Ile",
"transcript": "ENST00000885056.1",
"protein_id": "ENSP00000555115.1",
"transcript_support_level": null,
"aa_start": 116,
"aa_end": null,
"aa_length": 141,
"cds_start": 346,
"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": "V",
"aa_alt": "I",
"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.274G>A",
"hgvs_p": "p.Val92Ile",
"transcript": "NM_001323012.3",
"protein_id": "NP_001309941.1",
"transcript_support_level": null,
"aa_start": 92,
"aa_end": null,
"aa_length": 117,
"cds_start": 274,
"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": "V",
"aa_alt": "I",
"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.274G>A",
"hgvs_p": "p.Val92Ile",
"transcript": "NM_001348696.2",
"protein_id": "NP_001335625.1",
"transcript_support_level": null,
"aa_start": 92,
"aa_end": null,
"aa_length": 117,
"cds_start": 274,
"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": "rs140690994",
"frequency_reference_population": 0.000027265382,
"hom_count_reference_population": 0,
"allele_count_reference_population": 44,
"gnomad_exomes_af": 0.0000280498,
"gnomad_genomes_af": 0.0000197259,
"gnomad_exomes_ac": 41,
"gnomad_genomes_ac": 3,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.0981563925743103,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.047,
"revel_prediction": "Benign",
"alphamissense_score": 0.0795,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.45,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.772,
"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.499G>A",
"hgvs_p": "p.Val167Ile"
}
],
"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
}