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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: 16-30756714-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=30756714&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "16",
"pos": 30756714,
"ref": "G",
"alt": "A",
"effect": "missense_variant,splice_region_variant",
"transcript": "NM_000294.3",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHKG2",
"gene_hgnc_id": 8931,
"hgvs_c": "c.926G>A",
"hgvs_p": "p.Arg309Gln",
"transcript": "NM_000294.3",
"protein_id": "NP_000285.1",
"transcript_support_level": null,
"aa_start": 309,
"aa_end": null,
"aa_length": 406,
"cds_start": 926,
"cds_end": null,
"cds_length": 1221,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000563588.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_000294.3"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHKG2",
"gene_hgnc_id": 8931,
"hgvs_c": "c.926G>A",
"hgvs_p": "p.Arg309Gln",
"transcript": "ENST00000563588.6",
"protein_id": "ENSP00000455607.1",
"transcript_support_level": 1,
"aa_start": 309,
"aa_end": null,
"aa_length": 406,
"cds_start": 926,
"cds_end": null,
"cds_length": 1221,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_000294.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000563588.6"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHKG2",
"gene_hgnc_id": 8931,
"hgvs_c": "c.938G>A",
"hgvs_p": "p.Arg313Gln",
"transcript": "ENST00000328273.11",
"protein_id": "ENSP00000329968.7",
"transcript_support_level": 5,
"aa_start": 313,
"aa_end": null,
"aa_length": 410,
"cds_start": 938,
"cds_end": null,
"cds_length": 1233,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000328273.11"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHKG2",
"gene_hgnc_id": 8931,
"hgvs_c": "c.938G>A",
"hgvs_p": "p.Arg313Gln",
"transcript": "ENST00000915464.1",
"protein_id": "ENSP00000585523.1",
"transcript_support_level": null,
"aa_start": 313,
"aa_end": null,
"aa_length": 410,
"cds_start": 938,
"cds_end": null,
"cds_length": 1233,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000915464.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHKG2",
"gene_hgnc_id": 8931,
"hgvs_c": "c.926G>A",
"hgvs_p": "p.Arg309Gln",
"transcript": "ENST00000866456.1",
"protein_id": "ENSP00000536515.1",
"transcript_support_level": null,
"aa_start": 309,
"aa_end": null,
"aa_length": 406,
"cds_start": 926,
"cds_end": null,
"cds_length": 1221,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000866456.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHKG2",
"gene_hgnc_id": 8931,
"hgvs_c": "c.926G>A",
"hgvs_p": "p.Arg309Gln",
"transcript": "ENST00000958863.1",
"protein_id": "ENSP00000628922.1",
"transcript_support_level": null,
"aa_start": 309,
"aa_end": null,
"aa_length": 406,
"cds_start": 926,
"cds_end": null,
"cds_length": 1221,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000958863.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHKG2",
"gene_hgnc_id": 8931,
"hgvs_c": "c.896G>A",
"hgvs_p": "p.Arg299Gln",
"transcript": "ENST00000866454.1",
"protein_id": "ENSP00000536513.1",
"transcript_support_level": null,
"aa_start": 299,
"aa_end": null,
"aa_length": 396,
"cds_start": 896,
"cds_end": null,
"cds_length": 1191,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000866454.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHKG2",
"gene_hgnc_id": 8931,
"hgvs_c": "c.860G>A",
"hgvs_p": "p.Arg287Gln",
"transcript": "ENST00000915462.1",
"protein_id": "ENSP00000585521.1",
"transcript_support_level": null,
"aa_start": 287,
"aa_end": null,
"aa_length": 384,
"cds_start": 860,
"cds_end": null,
"cds_length": 1155,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000915462.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHKG2",
"gene_hgnc_id": 8931,
"hgvs_c": "c.854G>A",
"hgvs_p": "p.Arg285Gln",
"transcript": "ENST00000866453.1",
"protein_id": "ENSP00000536512.1",
"transcript_support_level": null,
"aa_start": 285,
"aa_end": null,
"aa_length": 382,
"cds_start": 854,
"cds_end": null,
"cds_length": 1149,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000866453.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHKG2",
"gene_hgnc_id": 8931,
"hgvs_c": "c.926G>A",
"hgvs_p": "p.Arg309Gln",
"transcript": "NM_001172432.2",
"protein_id": "NP_001165903.1",
"transcript_support_level": null,
"aa_start": 309,
"aa_end": null,
"aa_length": 374,
"cds_start": 926,
"cds_end": null,
"cds_length": 1125,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001172432.2"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHKG2",
"gene_hgnc_id": 8931,
"hgvs_c": "c.926G>A",
"hgvs_p": "p.Arg309Gln",
"transcript": "ENST00000424889.7",
"protein_id": "ENSP00000388571.3",
"transcript_support_level": 2,
"aa_start": 309,
"aa_end": null,
"aa_length": 374,
"cds_start": 926,
"cds_end": null,
"cds_length": 1125,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000424889.7"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHKG2",
"gene_hgnc_id": 8931,
"hgvs_c": "c.926G>A",
"hgvs_p": "p.Arg309Gln",
"transcript": "ENST00000866455.1",
"protein_id": "ENSP00000536514.1",
"transcript_support_level": null,
"aa_start": 309,
"aa_end": null,
"aa_length": 340,
"cds_start": 926,
"cds_end": null,
"cds_length": 1023,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000866455.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHKG2",
"gene_hgnc_id": 8931,
"hgvs_c": "c.695G>A",
"hgvs_p": "p.Arg232Gln",
"transcript": "ENST00000958864.1",
"protein_id": "ENSP00000628923.1",
"transcript_support_level": null,
"aa_start": 232,
"aa_end": null,
"aa_length": 329,
"cds_start": 695,
"cds_end": null,
"cds_length": 990,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000958864.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHKG2",
"gene_hgnc_id": 8931,
"hgvs_c": "c.332G>A",
"hgvs_p": "p.Arg111Gln",
"transcript": "ENST00000915463.1",
"protein_id": "ENSP00000585522.1",
"transcript_support_level": null,
"aa_start": 111,
"aa_end": null,
"aa_length": 208,
"cds_start": 332,
"cds_end": null,
"cds_length": 627,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000915463.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHKG2",
"gene_hgnc_id": 8931,
"hgvs_c": "n.1259G>A",
"hgvs_p": null,
"transcript": "ENST00000563913.5",
"protein_id": null,
"transcript_support_level": 5,
"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": "ENST00000563913.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHKG2",
"gene_hgnc_id": 8931,
"hgvs_c": "n.1055G>A",
"hgvs_p": null,
"transcript": "ENST00000564838.5",
"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": "retained_intron",
"feature": "ENST00000564838.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHKG2",
"gene_hgnc_id": 8931,
"hgvs_c": "c.*197G>A",
"hgvs_p": null,
"transcript": "ENST00000565897.5",
"protein_id": "ENSP00000457359.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 265,
"cds_start": null,
"cds_end": null,
"cds_length": 798,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000565897.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHKG2",
"gene_hgnc_id": 8931,
"hgvs_c": "c.*231G>A",
"hgvs_p": null,
"transcript": "ENST00000565924.5",
"protein_id": "ENSP00000455091.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 253,
"cds_start": null,
"cds_end": null,
"cds_length": 764,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000565924.5"
}
],
"gene_symbol": "PHKG2",
"gene_hgnc_id": 8931,
"dbsnp": "rs572115942",
"frequency_reference_population": 0.000086743705,
"hom_count_reference_population": 0,
"allele_count_reference_population": 140,
"gnomad_exomes_af": 0.0000889312,
"gnomad_genomes_af": 0.0000657263,
"gnomad_exomes_ac": 130,
"gnomad_genomes_ac": 10,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.331802636384964,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.8640000224113464,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": 0.135,
"revel_prediction": "Benign",
"alphamissense_score": 0.1034,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.34,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 5.307,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.993733916693694,
"dbscsnv_ada_prediction": "Pathogenic",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 6,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PM5,PP3,PP5",
"acmg_by_gene": [
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PM2",
"PM5",
"PP3",
"PP5"
],
"verdict": "Likely_pathogenic",
"transcript": "NM_000294.3",
"gene_symbol": "PHKG2",
"hgnc_id": 8931,
"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.926G>A",
"hgvs_p": "p.Arg309Gln"
}
],
"clinvar_disease": "Glycogen storage disease IXc,Mauriac syndrome,not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "P:1 US:2",
"phenotype_combined": "not provided|Mauriac syndrome|Glycogen storage disease IXc|not specified",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}