← Back to variant description
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: 9-78304839-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=78304839&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PS1_Very_Strong",
"PS3",
"PP3_Moderate",
"PP5"
],
"effects": [
"missense_variant"
],
"gene_symbol": "PSAT1",
"hgnc_id": 19129,
"hgvs_c": "c.296C>T",
"hgvs_p": "p.Ala99Val",
"inheritance_mode": "AR,AD",
"pathogenic_score": 15,
"score": 15,
"transcript": "NM_058179.4",
"verdict": "Pathogenic"
}
],
"acmg_classification": "Pathogenic",
"acmg_criteria": "PS1_Very_Strong,PS3,PP3_Moderate,PP5",
"acmg_score": 15,
"allele_count_reference_population": 440,
"alphamissense_prediction": null,
"alphamissense_score": 0.3281,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Uncertain_significance",
"bayesdelnoaf_score": 0.08,
"chr": "9",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_disease": "Neu-Laxova syndrome 2,PSAT1-related disorder,not provided",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:1 LP:3 O:1",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.8694624900817871,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 370,
"aa_ref": "A",
"aa_start": 99,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2206,
"cdna_start": 382,
"cds_end": null,
"cds_length": 1113,
"cds_start": 296,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "NM_058179.4",
"gene_hgnc_id": 19129,
"gene_symbol": "PSAT1",
"hgvs_c": "c.296C>T",
"hgvs_p": "p.Ala99Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000376588.4",
"protein_coding": true,
"protein_id": "NP_478059.1",
"strand": true,
"transcript": "NM_058179.4",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 370,
"aa_ref": "A",
"aa_start": 99,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2206,
"cdna_start": 382,
"cds_end": null,
"cds_length": 1113,
"cds_start": 296,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000376588.4",
"gene_hgnc_id": 19129,
"gene_symbol": "PSAT1",
"hgvs_c": "c.296C>T",
"hgvs_p": "p.Ala99Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_058179.4",
"protein_coding": true,
"protein_id": "ENSP00000365773.3",
"strand": true,
"transcript": "ENST00000376588.4",
"transcript_support_level": 1
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 324,
"aa_ref": "A",
"aa_start": 99,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1411,
"cdna_start": 364,
"cds_end": null,
"cds_length": 975,
"cds_start": 296,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000347159.6",
"gene_hgnc_id": 19129,
"gene_symbol": "PSAT1",
"hgvs_c": "c.296C>T",
"hgvs_p": "p.Ala99Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000317606.2",
"strand": true,
"transcript": "ENST00000347159.6",
"transcript_support_level": 1
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 367,
"aa_ref": "A",
"aa_start": 99,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2159,
"cdna_start": 347,
"cds_end": null,
"cds_length": 1104,
"cds_start": 296,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000906296.1",
"gene_hgnc_id": 19129,
"gene_symbol": "PSAT1",
"hgvs_c": "c.296C>T",
"hgvs_p": "p.Ala99Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000576355.1",
"strand": true,
"transcript": "ENST00000906296.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 358,
"aa_ref": "A",
"aa_start": 99,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2164,
"cdna_start": 376,
"cds_end": null,
"cds_length": 1077,
"cds_start": 296,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000916773.1",
"gene_hgnc_id": 19129,
"gene_symbol": "PSAT1",
"hgvs_c": "c.296C>T",
"hgvs_p": "p.Ala99Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000586832.1",
"strand": true,
"transcript": "ENST00000916773.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 356,
"aa_ref": "A",
"aa_start": 85,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2159,
"cdna_start": 338,
"cds_end": null,
"cds_length": 1071,
"cds_start": 254,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000906295.1",
"gene_hgnc_id": 19129,
"gene_symbol": "PSAT1",
"hgvs_c": "c.254C>T",
"hgvs_p": "p.Ala85Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000576354.1",
"strand": true,
"transcript": "ENST00000906295.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 327,
"aa_ref": "A",
"aa_start": 99,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2077,
"cdna_start": 382,
"cds_end": null,
"cds_length": 984,
"cds_start": 296,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000916771.1",
"gene_hgnc_id": 19129,
"gene_symbol": "PSAT1",
"hgvs_c": "c.296C>T",
"hgvs_p": "p.Ala99Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000586830.1",
"strand": true,
"transcript": "ENST00000916771.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 324,
"aa_ref": "A",
"aa_start": 99,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2068,
"cdna_start": 382,
"cds_end": null,
"cds_length": 975,
"cds_start": 296,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "NM_021154.5",
"gene_hgnc_id": 19129,
"gene_symbol": "PSAT1",
"hgvs_c": "c.296C>T",
"hgvs_p": "p.Ala99Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_066977.1",
"strand": true,
"transcript": "NM_021154.5",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 278,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1898,
"cdna_start": null,
"cds_end": null,
"cds_length": 837,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 7,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000916774.1",
"gene_hgnc_id": 19129,
"gene_symbol": "PSAT1",
"hgvs_c": "c.122-1475C>T",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000586833.1",
"strand": true,
"transcript": "ENST00000916774.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 187,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1688,
"cdna_start": null,
"cds_end": null,
"cds_length": 564,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 6,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000906293.1",
"gene_hgnc_id": 19129,
"gene_symbol": "PSAT1",
"hgvs_c": "c.191+2816C>T",
"hgvs_p": null,
"intron_rank": 3,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000576352.1",
"strand": true,
"transcript": "ENST00000906293.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 144,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1526,
"cdna_start": null,
"cds_end": null,
"cds_length": 435,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000906294.1",
"gene_hgnc_id": 19129,
"gene_symbol": "PSAT1",
"hgvs_c": "c.191+2816C>T",
"hgvs_p": null,
"intron_rank": 3,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000576353.1",
"strand": true,
"transcript": "ENST00000906294.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 141,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1524,
"cdna_start": null,
"cds_end": null,
"cds_length": 426,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000916770.1",
"gene_hgnc_id": 19129,
"gene_symbol": "PSAT1",
"hgvs_c": "c.191+2816C>T",
"hgvs_p": null,
"intron_rank": 3,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000586829.1",
"strand": true,
"transcript": "ENST00000916770.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 98,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1388,
"cdna_start": null,
"cds_end": null,
"cds_length": 297,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000916772.1",
"gene_hgnc_id": 19129,
"gene_symbol": "PSAT1",
"hgvs_c": "c.191+2816C>T",
"hgvs_p": null,
"intron_rank": 3,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000586831.1",
"strand": true,
"transcript": "ENST00000916772.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs587777778",
"effect": "missense_variant",
"frequency_reference_population": 0.0002726089,
"gene_hgnc_id": 19129,
"gene_symbol": "PSAT1",
"gnomad_exomes_ac": 412,
"gnomad_exomes_af": 0.00028183,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 28,
"gnomad_genomes_af": 0.000184017,
"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": "Pathogenic/Likely pathogenic",
"phenotype_combined": "Neu-Laxova syndrome 2|not provided|PSAT1-related disorder",
"phylop100way_prediction": "Pathogenic",
"phylop100way_score": 7.539,
"pos": 78304839,
"ref": "C",
"revel_prediction": "Pathogenic",
"revel_score": 0.881,
"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_058179.4"
}
]
}