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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: 8-90996715-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=8&pos=90996715&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "PIP4P2",
"hgnc_id": 25452,
"hgvs_c": "c.569G>C",
"hgvs_p": "p.Arg190Thr",
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": 2,
"transcript": "NM_018710.3",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_score": 2,
"allele_count_reference_population": 30,
"alphamissense_prediction": null,
"alphamissense_score": 0.6516,
"alt": "G",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Uncertain_significance",
"bayesdelnoaf_score": 0.07,
"chr": "8",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Uncertain_significance",
"computational_score_selected": 0.5994589924812317,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 257,
"aa_ref": "R",
"aa_start": 190,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2759,
"cdna_start": 679,
"cds_end": null,
"cds_length": 774,
"cds_start": 569,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "NM_018710.3",
"gene_hgnc_id": 25452,
"gene_symbol": "PIP4P2",
"hgvs_c": "c.569G>C",
"hgvs_p": "p.Arg190Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000285419.8",
"protein_coding": true,
"protein_id": "NP_061180.1",
"strand": false,
"transcript": "NM_018710.3",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 257,
"aa_ref": "R",
"aa_start": 190,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2759,
"cdna_start": 679,
"cds_end": null,
"cds_length": 774,
"cds_start": 569,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000285419.8",
"gene_hgnc_id": 25452,
"gene_symbol": "PIP4P2",
"hgvs_c": "c.569G>C",
"hgvs_p": "p.Arg190Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_018710.3",
"protein_coding": true,
"protein_id": "ENSP00000285419.3",
"strand": false,
"transcript": "ENST00000285419.8",
"transcript_support_level": 1
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 257,
"aa_ref": "R",
"aa_start": 190,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2502,
"cdna_start": 713,
"cds_end": null,
"cds_length": 774,
"cds_start": 569,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000886895.1",
"gene_hgnc_id": 25452,
"gene_symbol": "PIP4P2",
"hgvs_c": "c.569G>C",
"hgvs_p": "p.Arg190Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000556954.1",
"strand": false,
"transcript": "ENST00000886895.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 257,
"aa_ref": "R",
"aa_start": 190,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1482,
"cdna_start": 682,
"cds_end": null,
"cds_length": 774,
"cds_start": 569,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000886896.1",
"gene_hgnc_id": 25452,
"gene_symbol": "PIP4P2",
"hgvs_c": "c.569G>C",
"hgvs_p": "p.Arg190Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000556955.1",
"strand": false,
"transcript": "ENST00000886896.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 249,
"aa_ref": "R",
"aa_start": 196,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 838,
"cdna_start": 673,
"cds_end": null,
"cds_length": 752,
"cds_start": 587,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000520014.1",
"gene_hgnc_id": 25452,
"gene_symbol": "PIP4P2",
"hgvs_c": "c.587G>C",
"hgvs_p": "p.Arg196Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000427974.1",
"strand": false,
"transcript": "ENST00000520014.1",
"transcript_support_level": 5
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 240,
"aa_ref": "R",
"aa_start": 173,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2262,
"cdna_start": 650,
"cds_end": null,
"cds_length": 723,
"cds_start": 518,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000920106.1",
"gene_hgnc_id": 25452,
"gene_symbol": "PIP4P2",
"hgvs_c": "c.518G>C",
"hgvs_p": "p.Arg173Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000590165.1",
"strand": false,
"transcript": "ENST00000920106.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 234,
"aa_ref": "R",
"aa_start": 167,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2369,
"cdna_start": 758,
"cds_end": null,
"cds_length": 705,
"cds_start": 500,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000886897.1",
"gene_hgnc_id": 25452,
"gene_symbol": "PIP4P2",
"hgvs_c": "c.500G>C",
"hgvs_p": "p.Arg167Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000556956.1",
"strand": false,
"transcript": "ENST00000886897.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 234,
"aa_ref": "R",
"aa_start": 167,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2397,
"cdna_start": 611,
"cds_end": null,
"cds_length": 705,
"cds_start": 500,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000920105.1",
"gene_hgnc_id": 25452,
"gene_symbol": "PIP4P2",
"hgvs_c": "c.500G>C",
"hgvs_p": "p.Arg167Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000590164.1",
"strand": false,
"transcript": "ENST00000920105.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 867,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 6,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000518359.5",
"gene_hgnc_id": 25452,
"gene_symbol": "PIP4P2",
"hgvs_c": "n.*15G>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000429280.1",
"strand": false,
"transcript": "ENST00000518359.5",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 841,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 8,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000518869.1",
"gene_hgnc_id": 25452,
"gene_symbol": "PIP4P2",
"hgvs_c": "n.*476G>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000429112.1",
"strand": false,
"transcript": "ENST00000518869.1",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 649,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 4,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000520709.5",
"gene_hgnc_id": 25452,
"gene_symbol": "PIP4P2",
"hgvs_c": "n.*15G>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000430707.1",
"strand": false,
"transcript": "ENST00000520709.5",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 867,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 6,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000518359.5",
"gene_hgnc_id": 25452,
"gene_symbol": "PIP4P2",
"hgvs_c": "n.*15G>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000429280.1",
"strand": false,
"transcript": "ENST00000518359.5",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 841,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 8,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000518869.1",
"gene_hgnc_id": 25452,
"gene_symbol": "PIP4P2",
"hgvs_c": "n.*476G>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000429112.1",
"strand": false,
"transcript": "ENST00000518869.1",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 649,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 4,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000520709.5",
"gene_hgnc_id": 25452,
"gene_symbol": "PIP4P2",
"hgvs_c": "n.*15G>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000430707.1",
"strand": false,
"transcript": "ENST00000520709.5",
"transcript_support_level": 3
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs775495620",
"effect": "missense_variant",
"frequency_reference_population": 0.000018640789,
"gene_hgnc_id": 25452,
"gene_symbol": "PIP4P2",
"gnomad_exomes_ac": 27,
"gnomad_exomes_af": 0.0000185282,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 3,
"gnomad_genomes_af": 0.0000197195,
"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": "Uncertain significance",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Pathogenic",
"phylop100way_score": 7.568,
"pos": 90996715,
"ref": "C",
"revel_prediction": "Uncertain_significance",
"revel_score": 0.358,
"splice_prediction_selected": "Uncertain_significance",
"splice_score_selected": 0.2800000011920929,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Uncertain_significance",
"spliceai_max_score": 0.28,
"transcript": "NM_018710.3"
}
]
}