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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: 3-196820434-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=196820434&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM2",
"PP2",
"PP3_Strong"
],
"effects": [
"missense_variant"
],
"gene_symbol": "PAK2",
"hgnc_id": 8591,
"hgvs_c": "c.1217C>T",
"hgvs_p": "p.Thr406Met",
"inheritance_mode": "Unknown,AD",
"pathogenic_score": 7,
"score": 7,
"transcript": "NM_002577.4",
"verdict": "Likely_pathogenic"
}
],
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PP2,PP3_Strong",
"acmg_score": 7,
"allele_count_reference_population": 1,
"alphamissense_prediction": "Pathogenic",
"alphamissense_score": 0.9997,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.21,
"chr": "3",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not provided",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.9804250001907349,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 524,
"aa_ref": "T",
"aa_start": 406,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6139,
"cdna_start": 1539,
"cds_end": null,
"cds_length": 1575,
"cds_start": 1217,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "NM_002577.4",
"gene_hgnc_id": 8591,
"gene_symbol": "PAK2",
"hgvs_c": "c.1217C>T",
"hgvs_p": "p.Thr406Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000327134.7",
"protein_coding": true,
"protein_id": "NP_002568.2",
"strand": true,
"transcript": "NM_002577.4",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 524,
"aa_ref": "T",
"aa_start": 406,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 6139,
"cdna_start": 1539,
"cds_end": null,
"cds_length": 1575,
"cds_start": 1217,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000327134.7",
"gene_hgnc_id": 8591,
"gene_symbol": "PAK2",
"hgvs_c": "c.1217C>T",
"hgvs_p": "p.Thr406Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_002577.4",
"protein_coding": true,
"protein_id": "ENSP00000314067.3",
"strand": true,
"transcript": "ENST00000327134.7",
"transcript_support_level": 2
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 524,
"aa_ref": "T",
"aa_start": 406,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6213,
"cdna_start": 1772,
"cds_end": null,
"cds_length": 1575,
"cds_start": 1217,
"consequences": [
"missense_variant"
],
"exon_count": 16,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "ENST00000871388.1",
"gene_hgnc_id": 8591,
"gene_symbol": "PAK2",
"hgvs_c": "c.1217C>T",
"hgvs_p": "p.Thr406Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000541447.1",
"strand": true,
"transcript": "ENST00000871388.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 524,
"aa_ref": "T",
"aa_start": 406,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3942,
"cdna_start": 1736,
"cds_end": null,
"cds_length": 1575,
"cds_start": 1217,
"consequences": [
"missense_variant"
],
"exon_count": 16,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "ENST00000871391.1",
"gene_hgnc_id": 8591,
"gene_symbol": "PAK2",
"hgvs_c": "c.1217C>T",
"hgvs_p": "p.Thr406Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000541450.1",
"strand": true,
"transcript": "ENST00000871391.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 524,
"aa_ref": "T",
"aa_start": 406,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3402,
"cdna_start": 1672,
"cds_end": null,
"cds_length": 1575,
"cds_start": 1217,
"consequences": [
"missense_variant"
],
"exon_count": 16,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "ENST00000959937.1",
"gene_hgnc_id": 8591,
"gene_symbol": "PAK2",
"hgvs_c": "c.1217C>T",
"hgvs_p": "p.Thr406Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000629996.1",
"strand": true,
"transcript": "ENST00000959937.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 483,
"aa_ref": "T",
"aa_start": 365,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4046,
"cdna_start": 1395,
"cds_end": null,
"cds_length": 1452,
"cds_start": 1094,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000871389.1",
"gene_hgnc_id": 8591,
"gene_symbol": "PAK2",
"hgvs_c": "c.1094C>T",
"hgvs_p": "p.Thr365Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000541448.1",
"strand": true,
"transcript": "ENST00000871389.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 478,
"aa_ref": "T",
"aa_start": 406,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4001,
"cdna_start": 1493,
"cds_end": null,
"cds_length": 1437,
"cds_start": 1217,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000871390.1",
"gene_hgnc_id": 8591,
"gene_symbol": "PAK2",
"hgvs_c": "c.1217C>T",
"hgvs_p": "p.Thr406Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000541449.1",
"strand": true,
"transcript": "ENST00000871390.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 478,
"aa_ref": "T",
"aa_start": 406,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4198,
"cdna_start": 1687,
"cds_end": null,
"cds_length": 1437,
"cds_start": 1217,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "ENST00000959935.1",
"gene_hgnc_id": 8591,
"gene_symbol": "PAK2",
"hgvs_c": "c.1217C>T",
"hgvs_p": "p.Thr406Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000629994.1",
"strand": true,
"transcript": "ENST00000959935.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 441,
"aa_ref": "T",
"aa_start": 323,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3493,
"cdna_start": 1296,
"cds_end": null,
"cds_length": 1326,
"cds_start": 968,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000959936.1",
"gene_hgnc_id": 8591,
"gene_symbol": "PAK2",
"hgvs_c": "c.968C>T",
"hgvs_p": "p.Thr323Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000629995.1",
"strand": true,
"transcript": "ENST00000959936.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 433,
"aa_ref": "T",
"aa_start": 315,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5444,
"cdna_start": 1010,
"cds_end": null,
"cds_length": 1302,
"cds_start": 944,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000915912.1",
"gene_hgnc_id": 8591,
"gene_symbol": "PAK2",
"hgvs_c": "c.944C>T",
"hgvs_p": "p.Thr315Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000585971.1",
"strand": true,
"transcript": "ENST00000915912.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 220,
"aa_ref": "T",
"aa_start": 148,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 689,
"cdna_start": 445,
"cds_end": null,
"cds_length": 663,
"cds_start": 443,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000426668.1",
"gene_hgnc_id": 8591,
"gene_symbol": "PAK2",
"hgvs_c": "c.443C>T",
"hgvs_p": "p.Thr148Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000402927.1",
"strand": true,
"transcript": "ENST00000426668.1",
"transcript_support_level": 3
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 524,
"aa_ref": "T",
"aa_start": 406,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5954,
"cdna_start": 1354,
"cds_end": null,
"cds_length": 1575,
"cds_start": 1217,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "XM_011512870.3",
"gene_hgnc_id": 8591,
"gene_symbol": "PAK2",
"hgvs_c": "c.1217C>T",
"hgvs_p": "p.Thr406Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011511172.1",
"strand": true,
"transcript": "XM_011512870.3",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 524,
"aa_ref": "T",
"aa_start": 406,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6021,
"cdna_start": 1421,
"cds_end": null,
"cds_length": 1575,
"cds_start": 1217,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "XM_047448218.1",
"gene_hgnc_id": 8591,
"gene_symbol": "PAK2",
"hgvs_c": "c.1217C>T",
"hgvs_p": "p.Thr406Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047304174.1",
"strand": true,
"transcript": "XM_047448218.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 524,
"aa_ref": "T",
"aa_start": 406,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5984,
"cdna_start": 1384,
"cds_end": null,
"cds_length": 1575,
"cds_start": 1217,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "XM_047448219.1",
"gene_hgnc_id": 8591,
"gene_symbol": "PAK2",
"hgvs_c": "c.1217C>T",
"hgvs_p": "p.Thr406Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047304175.1",
"strand": true,
"transcript": "XM_047448219.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 425,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5690,
"cdna_start": null,
"cds_end": null,
"cds_length": 1278,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 13,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000915911.1",
"gene_hgnc_id": 8591,
"gene_symbol": "PAK2",
"hgvs_c": "c.1053+5866C>T",
"hgvs_p": null,
"intron_rank": 11,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000585970.1",
"strand": true,
"transcript": "ENST00000915911.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs1442050261",
"effect": "missense_variant",
"frequency_reference_population": 0.000006574017,
"gene_hgnc_id": 8591,
"gene_symbol": "PAK2",
"gnomad_exomes_ac": 0,
"gnomad_exomes_af": 0,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 1,
"gnomad_genomes_af": 0.00000657402,
"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 provided",
"phylop100way_prediction": "Pathogenic",
"phylop100way_score": 7.568,
"pos": 196820434,
"ref": "C",
"revel_prediction": "Uncertain_significance",
"revel_score": 0.6,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_002577.4"
}
]
}