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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: 16-30756927-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=30756927&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 1,
"criteria": [
"BP6"
],
"effects": [
"missense_variant"
],
"gene_symbol": "PHKG2",
"hgnc_id": 8931,
"hgvs_c": "c.1051G>A",
"hgvs_p": "p.Asp351Asn",
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -1,
"transcript": "NM_000294.3",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP6",
"acmg_score": -1,
"allele_count_reference_population": 90,
"alphamissense_prediction": null,
"alphamissense_score": 0.9163,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.32,
"chr": "16",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_disease": "Glycogen storage disease IXc,not provided",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:3 LB:1",
"computational_prediction_selected": "Uncertain_significance",
"computational_score_selected": 0.547001838684082,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 406,
"aa_ref": "D",
"aa_start": 351,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5384,
"cdna_start": 1135,
"cds_end": null,
"cds_length": 1221,
"cds_start": 1051,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "NM_000294.3",
"gene_hgnc_id": 8931,
"gene_symbol": "PHKG2",
"hgvs_c": "c.1051G>A",
"hgvs_p": "p.Asp351Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000563588.6",
"protein_coding": true,
"protein_id": "NP_000285.1",
"strand": true,
"transcript": "NM_000294.3",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 406,
"aa_ref": "D",
"aa_start": 351,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 5384,
"cdna_start": 1135,
"cds_end": null,
"cds_length": 1221,
"cds_start": 1051,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000563588.6",
"gene_hgnc_id": 8931,
"gene_symbol": "PHKG2",
"hgvs_c": "c.1051G>A",
"hgvs_p": "p.Asp351Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_000294.3",
"protein_coding": true,
"protein_id": "ENSP00000455607.1",
"strand": true,
"transcript": "ENST00000563588.6",
"transcript_support_level": 1
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 410,
"aa_ref": "D",
"aa_start": 355,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1536,
"cdna_start": 1132,
"cds_end": null,
"cds_length": 1233,
"cds_start": 1063,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000328273.11",
"gene_hgnc_id": 8931,
"gene_symbol": "PHKG2",
"hgvs_c": "c.1063G>A",
"hgvs_p": "p.Asp355Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000329968.7",
"strand": true,
"transcript": "ENST00000328273.11",
"transcript_support_level": 5
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 410,
"aa_ref": "D",
"aa_start": 355,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1795,
"cdna_start": 1355,
"cds_end": null,
"cds_length": 1233,
"cds_start": 1063,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000915464.1",
"gene_hgnc_id": 8931,
"gene_symbol": "PHKG2",
"hgvs_c": "c.1063G>A",
"hgvs_p": "p.Asp355Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000585523.1",
"strand": true,
"transcript": "ENST00000915464.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 406,
"aa_ref": "D",
"aa_start": 351,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1533,
"cdna_start": 1099,
"cds_end": null,
"cds_length": 1221,
"cds_start": 1051,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000866456.1",
"gene_hgnc_id": 8931,
"gene_symbol": "PHKG2",
"hgvs_c": "c.1051G>A",
"hgvs_p": "p.Asp351Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000536515.1",
"strand": true,
"transcript": "ENST00000866456.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 406,
"aa_ref": "D",
"aa_start": 351,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1629,
"cdna_start": 1199,
"cds_end": null,
"cds_length": 1221,
"cds_start": 1051,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000958863.1",
"gene_hgnc_id": 8931,
"gene_symbol": "PHKG2",
"hgvs_c": "c.1051G>A",
"hgvs_p": "p.Asp351Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000628922.1",
"strand": true,
"transcript": "ENST00000958863.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 396,
"aa_ref": "D",
"aa_start": 341,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1549,
"cdna_start": 1114,
"cds_end": null,
"cds_length": 1191,
"cds_start": 1021,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000866454.1",
"gene_hgnc_id": 8931,
"gene_symbol": "PHKG2",
"hgvs_c": "c.1021G>A",
"hgvs_p": "p.Asp341Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000536513.1",
"strand": true,
"transcript": "ENST00000866454.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 384,
"aa_ref": "D",
"aa_start": 329,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1519,
"cdna_start": 1087,
"cds_end": null,
"cds_length": 1155,
"cds_start": 985,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000915462.1",
"gene_hgnc_id": 8931,
"gene_symbol": "PHKG2",
"hgvs_c": "c.985G>A",
"hgvs_p": "p.Asp329Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000585521.1",
"strand": true,
"transcript": "ENST00000915462.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 382,
"aa_ref": "D",
"aa_start": 327,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1523,
"cdna_start": 1089,
"cds_end": null,
"cds_length": 1149,
"cds_start": 979,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000866453.1",
"gene_hgnc_id": 8931,
"gene_symbol": "PHKG2",
"hgvs_c": "c.979G>A",
"hgvs_p": "p.Asp327Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000536512.1",
"strand": true,
"transcript": "ENST00000866453.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 374,
"aa_ref": "D",
"aa_start": 351,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2225,
"cdna_start": 1135,
"cds_end": null,
"cds_length": 1125,
"cds_start": 1051,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "NM_001172432.2",
"gene_hgnc_id": 8931,
"gene_symbol": "PHKG2",
"hgvs_c": "c.1051G>A",
"hgvs_p": "p.Asp351Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001165903.1",
"strand": true,
"transcript": "NM_001172432.2",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 374,
"aa_ref": "D",
"aa_start": 351,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1566,
"cdna_start": 1261,
"cds_end": null,
"cds_length": 1125,
"cds_start": 1051,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000424889.7",
"gene_hgnc_id": 8931,
"gene_symbol": "PHKG2",
"hgvs_c": "c.1051G>A",
"hgvs_p": "p.Asp351Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000388571.3",
"strand": true,
"transcript": "ENST00000424889.7",
"transcript_support_level": 2
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 329,
"aa_ref": "D",
"aa_start": 274,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1312,
"cdna_start": 881,
"cds_end": null,
"cds_length": 990,
"cds_start": 820,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000958864.1",
"gene_hgnc_id": 8931,
"gene_symbol": "PHKG2",
"hgvs_c": "c.820G>A",
"hgvs_p": "p.Asp274Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000628923.1",
"strand": true,
"transcript": "ENST00000958864.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 208,
"aa_ref": "D",
"aa_start": 153,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 968,
"cdna_start": 537,
"cds_end": null,
"cds_length": 627,
"cds_start": 457,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000915463.1",
"gene_hgnc_id": 8931,
"gene_symbol": "PHKG2",
"hgvs_c": "c.457G>A",
"hgvs_p": "p.Asp153Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000585522.1",
"strand": true,
"transcript": "ENST00000915463.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 340,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1365,
"cdna_start": null,
"cds_end": null,
"cds_length": 1023,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 10,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000866455.1",
"gene_hgnc_id": 8931,
"gene_symbol": "PHKG2",
"hgvs_c": "c.928-75G>A",
"hgvs_p": null,
"intron_rank": 9,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000536514.1",
"strand": true,
"transcript": "ENST00000866455.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 1791,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 9,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000563913.5",
"gene_hgnc_id": 8931,
"gene_symbol": "PHKG2",
"hgvs_c": "n.1384G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000563913.5",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 1618,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000564838.5",
"gene_hgnc_id": 8931,
"gene_symbol": "PHKG2",
"hgvs_c": "n.1180G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000564838.5",
"transcript_support_level": 2
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs151033581",
"effect": "missense_variant",
"frequency_reference_population": 0.000055768993,
"gene_hgnc_id": 8931,
"gene_symbol": "PHKG2",
"gnomad_exomes_ac": 73,
"gnomad_exomes_af": 0.0000499438,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 17,
"gnomad_genomes_af": 0.000111726,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"phenotype_combined": "Glycogen storage disease IXc|not provided",
"phylop100way_prediction": "Pathogenic",
"phylop100way_score": 10.003,
"pos": 30756927,
"ref": "G",
"revel_prediction": "Uncertain_significance",
"revel_score": 0.39,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.009999999776482582,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.01,
"transcript": "NM_000294.3"
}
]
}