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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: 3-196810598-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=196810598&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 196810598,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_002577.4",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAK2",
"gene_hgnc_id": 8591,
"hgvs_c": "c.718G>A",
"hgvs_p": "p.Val240Met",
"transcript": "NM_002577.4",
"protein_id": "NP_002568.2",
"transcript_support_level": null,
"aa_start": 240,
"aa_end": null,
"aa_length": 524,
"cds_start": 718,
"cds_end": null,
"cds_length": 1575,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000327134.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_002577.4"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAK2",
"gene_hgnc_id": 8591,
"hgvs_c": "c.718G>A",
"hgvs_p": "p.Val240Met",
"transcript": "ENST00000327134.7",
"protein_id": "ENSP00000314067.3",
"transcript_support_level": 2,
"aa_start": 240,
"aa_end": null,
"aa_length": 524,
"cds_start": 718,
"cds_end": null,
"cds_length": 1575,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_002577.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000327134.7"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAK2",
"gene_hgnc_id": 8591,
"hgvs_c": "c.718G>A",
"hgvs_p": "p.Val240Met",
"transcript": "ENST00000871388.1",
"protein_id": "ENSP00000541447.1",
"transcript_support_level": null,
"aa_start": 240,
"aa_end": null,
"aa_length": 524,
"cds_start": 718,
"cds_end": null,
"cds_length": 1575,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000871388.1"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAK2",
"gene_hgnc_id": 8591,
"hgvs_c": "c.718G>A",
"hgvs_p": "p.Val240Met",
"transcript": "ENST00000871391.1",
"protein_id": "ENSP00000541450.1",
"transcript_support_level": null,
"aa_start": 240,
"aa_end": null,
"aa_length": 524,
"cds_start": 718,
"cds_end": null,
"cds_length": 1575,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000871391.1"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAK2",
"gene_hgnc_id": 8591,
"hgvs_c": "c.718G>A",
"hgvs_p": "p.Val240Met",
"transcript": "ENST00000959937.1",
"protein_id": "ENSP00000629996.1",
"transcript_support_level": null,
"aa_start": 240,
"aa_end": null,
"aa_length": 524,
"cds_start": 718,
"cds_end": null,
"cds_length": 1575,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000959937.1"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAK2",
"gene_hgnc_id": 8591,
"hgvs_c": "c.718G>A",
"hgvs_p": "p.Val240Met",
"transcript": "ENST00000871389.1",
"protein_id": "ENSP00000541448.1",
"transcript_support_level": null,
"aa_start": 240,
"aa_end": null,
"aa_length": 483,
"cds_start": 718,
"cds_end": null,
"cds_length": 1452,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000871389.1"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAK2",
"gene_hgnc_id": 8591,
"hgvs_c": "c.718G>A",
"hgvs_p": "p.Val240Met",
"transcript": "ENST00000871390.1",
"protein_id": "ENSP00000541449.1",
"transcript_support_level": null,
"aa_start": 240,
"aa_end": null,
"aa_length": 478,
"cds_start": 718,
"cds_end": null,
"cds_length": 1437,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000871390.1"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAK2",
"gene_hgnc_id": 8591,
"hgvs_c": "c.718G>A",
"hgvs_p": "p.Val240Met",
"transcript": "ENST00000959935.1",
"protein_id": "ENSP00000629994.1",
"transcript_support_level": null,
"aa_start": 240,
"aa_end": null,
"aa_length": 478,
"cds_start": 718,
"cds_end": null,
"cds_length": 1437,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000959935.1"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAK2",
"gene_hgnc_id": 8591,
"hgvs_c": "c.469G>A",
"hgvs_p": "p.Val157Met",
"transcript": "ENST00000959936.1",
"protein_id": "ENSP00000629995.1",
"transcript_support_level": null,
"aa_start": 157,
"aa_end": null,
"aa_length": 441,
"cds_start": 469,
"cds_end": null,
"cds_length": 1326,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000959936.1"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAK2",
"gene_hgnc_id": 8591,
"hgvs_c": "c.445G>A",
"hgvs_p": "p.Val149Met",
"transcript": "ENST00000915912.1",
"protein_id": "ENSP00000585971.1",
"transcript_support_level": null,
"aa_start": 149,
"aa_end": null,
"aa_length": 433,
"cds_start": 445,
"cds_end": null,
"cds_length": 1302,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000915912.1"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAK2",
"gene_hgnc_id": 8591,
"hgvs_c": "c.718G>A",
"hgvs_p": "p.Val240Met",
"transcript": "ENST00000915911.1",
"protein_id": "ENSP00000585970.1",
"transcript_support_level": null,
"aa_start": 240,
"aa_end": null,
"aa_length": 425,
"cds_start": 718,
"cds_end": null,
"cds_length": 1278,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000915911.1"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAK2",
"gene_hgnc_id": 8591,
"hgvs_c": "c.718G>A",
"hgvs_p": "p.Val240Met",
"transcript": "XM_011512870.3",
"protein_id": "XP_011511172.1",
"transcript_support_level": null,
"aa_start": 240,
"aa_end": null,
"aa_length": 524,
"cds_start": 718,
"cds_end": null,
"cds_length": 1575,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011512870.3"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAK2",
"gene_hgnc_id": 8591,
"hgvs_c": "c.718G>A",
"hgvs_p": "p.Val240Met",
"transcript": "XM_047448218.1",
"protein_id": "XP_047304174.1",
"transcript_support_level": null,
"aa_start": 240,
"aa_end": null,
"aa_length": 524,
"cds_start": 718,
"cds_end": null,
"cds_length": 1575,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047448218.1"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAK2",
"gene_hgnc_id": 8591,
"hgvs_c": "c.718G>A",
"hgvs_p": "p.Val240Met",
"transcript": "XM_047448219.1",
"protein_id": "XP_047304175.1",
"transcript_support_level": null,
"aa_start": 240,
"aa_end": null,
"aa_length": 524,
"cds_start": 718,
"cds_end": null,
"cds_length": 1575,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047448219.1"
}
],
"gene_symbol": "PAK2",
"gene_hgnc_id": 8591,
"dbsnp": "rs757747754",
"frequency_reference_population": 0.0000049609853,
"hom_count_reference_population": 0,
"allele_count_reference_population": 7,
"gnomad_exomes_af": 0.00000496099,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 7,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.7848477363586426,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.029999999329447746,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.399,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.9987,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": -0.04,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 9.484,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.03,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PP2,PP3,BS2",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PP2",
"PP3",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "NM_002577.4",
"gene_symbol": "PAK2",
"hgnc_id": 8591,
"effects": [
"missense_variant"
],
"inheritance_mode": "Unknown,AD",
"hgvs_c": "c.718G>A",
"hgvs_p": "p.Val240Met"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}