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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: 20-57563565-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=20&pos=57563565&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 20,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"effects": [
"missense_variant",
"splice_region_variant"
],
"gene_symbol": "PCK1",
"hgnc_id": 8724,
"hgvs_c": "c.799A>G",
"hgvs_p": "p.Ile267Val",
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -20,
"transcript": "NM_002591.4",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BA1",
"acmg_score": -20,
"allele_count_reference_population": 167969,
"alphamissense_prediction": "Benign",
"alphamissense_score": 0.2556,
"alt": "G",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.45,
"chr": "20",
"clinvar_classification": "Benign",
"clinvar_disease": " cytosolic,Phosphoenolpyruvate carboxykinase deficiency,not provided",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:4",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.0036648809909820557,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 622,
"aa_ref": "I",
"aa_start": 267,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4320,
"cdna_start": 933,
"cds_end": null,
"cds_length": 1869,
"cds_start": 799,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 10,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "NM_002591.4",
"gene_hgnc_id": 8724,
"gene_symbol": "PCK1",
"hgvs_c": "c.799A>G",
"hgvs_p": "p.Ile267Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000319441.6",
"protein_coding": true,
"protein_id": "NP_002582.3",
"strand": true,
"transcript": "NM_002591.4",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 622,
"aa_ref": "I",
"aa_start": 267,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 4320,
"cdna_start": 933,
"cds_end": null,
"cds_length": 1869,
"cds_start": 799,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 10,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000319441.6",
"gene_hgnc_id": 8724,
"gene_symbol": "PCK1",
"hgvs_c": "c.799A>G",
"hgvs_p": "p.Ile267Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_002591.4",
"protein_coding": true,
"protein_id": "ENSP00000319814.4",
"strand": true,
"transcript": "ENST00000319441.6",
"transcript_support_level": 1
},
{
"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": 5074,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 2,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000467047.1",
"gene_hgnc_id": 8724,
"gene_symbol": "PCK1",
"hgvs_c": "n.2486A>G",
"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": "ENST00000467047.1",
"transcript_support_level": 1
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 622,
"aa_ref": "I",
"aa_start": 267,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3364,
"cdna_start": 1638,
"cds_end": null,
"cds_length": 1869,
"cds_start": 799,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 9,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000851909.1",
"gene_hgnc_id": 8724,
"gene_symbol": "PCK1",
"hgvs_c": "c.799A>G",
"hgvs_p": "p.Ile267Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000521968.1",
"strand": true,
"transcript": "ENST00000851909.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 622,
"aa_ref": "I",
"aa_start": 267,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2701,
"cdna_start": 980,
"cds_end": null,
"cds_length": 1869,
"cds_start": 799,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 10,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000851910.1",
"gene_hgnc_id": 8724,
"gene_symbol": "PCK1",
"hgvs_c": "c.799A>G",
"hgvs_p": "p.Ile267Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000521969.1",
"strand": true,
"transcript": "ENST00000851910.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 622,
"aa_ref": "I",
"aa_start": 267,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2716,
"cdna_start": 1012,
"cds_end": null,
"cds_length": 1869,
"cds_start": 799,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 10,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000851913.1",
"gene_hgnc_id": 8724,
"gene_symbol": "PCK1",
"hgvs_c": "c.799A>G",
"hgvs_p": "p.Ile267Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000521972.1",
"strand": true,
"transcript": "ENST00000851913.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 618,
"aa_ref": "I",
"aa_start": 263,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2636,
"cdna_start": 921,
"cds_end": null,
"cds_length": 1857,
"cds_start": 787,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 10,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000851912.1",
"gene_hgnc_id": 8724,
"gene_symbol": "PCK1",
"hgvs_c": "c.787A>G",
"hgvs_p": "p.Ile263Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000521971.1",
"strand": true,
"transcript": "ENST00000851912.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 606,
"aa_ref": "I",
"aa_start": 267,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3285,
"cdna_start": 935,
"cds_end": null,
"cds_length": 1821,
"cds_start": 799,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 10,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000851908.1",
"gene_hgnc_id": 8724,
"gene_symbol": "PCK1",
"hgvs_c": "c.799A>G",
"hgvs_p": "p.Ile267Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000521967.1",
"strand": true,
"transcript": "ENST00000851908.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 490,
"aa_ref": "I",
"aa_start": 135,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4138,
"cdna_start": 751,
"cds_end": null,
"cds_length": 1473,
"cds_start": 403,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 9,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "XM_024451888.2",
"gene_hgnc_id": 8724,
"gene_symbol": "PCK1",
"hgvs_c": "c.403A>G",
"hgvs_p": "p.Ile135Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_024307656.1",
"strand": true,
"transcript": "XM_024451888.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 505,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2303,
"cdna_start": null,
"cds_end": null,
"cds_length": 1518,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 8,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000851911.1",
"gene_hgnc_id": 8724,
"gene_symbol": "PCK1",
"hgvs_c": "c.611-604A>G",
"hgvs_p": null,
"intron_rank": 4,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000521970.1",
"strand": true,
"transcript": "ENST00000851911.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 437,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2087,
"cdna_start": null,
"cds_end": null,
"cds_length": 1314,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 7,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000965008.1",
"gene_hgnc_id": 8724,
"gene_symbol": "PCK1",
"hgvs_c": "c.407-604A>G",
"hgvs_p": null,
"intron_rank": 3,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000635067.1",
"strand": true,
"transcript": "ENST00000965008.1",
"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": 409,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000470051.1",
"gene_hgnc_id": 8724,
"gene_symbol": "PCK1",
"hgvs_c": "n.383A>G",
"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": "ENST00000470051.1",
"transcript_support_level": 2
},
{
"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": 783,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000498194.1",
"gene_hgnc_id": 8724,
"gene_symbol": "PCK1",
"hgvs_c": "n.741A>G",
"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": "ENST00000498194.1",
"transcript_support_level": 2
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": "Benign",
"dbscsnv_ada_score": 0.151066856620867,
"dbsnp": "rs8192708",
"effect": "missense_variant,splice_region_variant",
"frequency_reference_population": 0.10547517,
"gene_hgnc_id": 8724,
"gene_symbol": "PCK1",
"gnomad_exomes_ac": 153945,
"gnomad_exomes_af": 0.106882,
"gnomad_exomes_homalt": 8958,
"gnomad_genomes_ac": 14024,
"gnomad_genomes_af": 0.0921625,
"gnomad_genomes_homalt": 756,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 9714,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Benign",
"phenotype_combined": "Phosphoenolpyruvate carboxykinase deficiency, cytosolic|not provided",
"phylop100way_prediction": "Pathogenic",
"phylop100way_score": 8.818,
"pos": 57563565,
"ref": "A",
"revel_prediction": "Benign",
"revel_score": 0.22,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.1979999989271164,
"splice_source_selected": "dbscSNV1_RF",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_002591.4"
}
]
}