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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: 1-7970934-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=7970934&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 7970934,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000338639.10",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PARK7",
"gene_hgnc_id": 16369,
"hgvs_c": "c.293G>A",
"hgvs_p": "p.Arg98Gln",
"transcript": "NM_007262.5",
"protein_id": "NP_009193.2",
"transcript_support_level": null,
"aa_start": 98,
"aa_end": null,
"aa_length": 189,
"cds_start": 293,
"cds_end": null,
"cds_length": 570,
"cdna_start": 399,
"cdna_end": null,
"cdna_length": 1127,
"mane_select": "ENST00000338639.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PARK7",
"gene_hgnc_id": 16369,
"hgvs_c": "c.293G>A",
"hgvs_p": "p.Arg98Gln",
"transcript": "ENST00000338639.10",
"protein_id": "ENSP00000340278.5",
"transcript_support_level": 1,
"aa_start": 98,
"aa_end": null,
"aa_length": 189,
"cds_start": 293,
"cds_end": null,
"cds_length": 570,
"cdna_start": 399,
"cdna_end": null,
"cdna_length": 1127,
"mane_select": "NM_007262.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PARK7",
"gene_hgnc_id": 16369,
"hgvs_c": "c.293G>A",
"hgvs_p": "p.Arg98Gln",
"transcript": "ENST00000493678.5",
"protein_id": "ENSP00000418770.1",
"transcript_support_level": 1,
"aa_start": 98,
"aa_end": null,
"aa_length": 189,
"cds_start": 293,
"cds_end": null,
"cds_length": 570,
"cdna_start": 360,
"cdna_end": null,
"cdna_length": 1088,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PARK7",
"gene_hgnc_id": 16369,
"hgvs_c": "c.293G>A",
"hgvs_p": "p.Arg98Gln",
"transcript": "NM_001123377.2",
"protein_id": "NP_001116849.1",
"transcript_support_level": null,
"aa_start": 98,
"aa_end": null,
"aa_length": 189,
"cds_start": 293,
"cds_end": null,
"cds_length": 570,
"cdna_start": 341,
"cdna_end": null,
"cdna_length": 1069,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PARK7",
"gene_hgnc_id": 16369,
"hgvs_c": "c.293G>A",
"hgvs_p": "p.Arg98Gln",
"transcript": "ENST00000377488.5",
"protein_id": "ENSP00000366708.1",
"transcript_support_level": 3,
"aa_start": 98,
"aa_end": null,
"aa_length": 189,
"cds_start": 293,
"cds_end": null,
"cds_length": 570,
"cdna_start": 449,
"cdna_end": null,
"cdna_length": 783,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PARK7",
"gene_hgnc_id": 16369,
"hgvs_c": "c.293G>A",
"hgvs_p": "p.Arg98Gln",
"transcript": "ENST00000377491.5",
"protein_id": "ENSP00000366711.1",
"transcript_support_level": 3,
"aa_start": 98,
"aa_end": null,
"aa_length": 189,
"cds_start": 293,
"cds_end": null,
"cds_length": 570,
"cdna_start": 504,
"cdna_end": null,
"cdna_length": 977,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PARK7",
"gene_hgnc_id": 16369,
"hgvs_c": "c.293G>A",
"hgvs_p": "p.Arg98Gln",
"transcript": "ENST00000493373.5",
"protein_id": "ENSP00000465404.1",
"transcript_support_level": 5,
"aa_start": 98,
"aa_end": null,
"aa_length": 188,
"cds_start": 293,
"cds_end": null,
"cds_length": 568,
"cdna_start": 349,
"cdna_end": null,
"cdna_length": 624,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PARK7",
"gene_hgnc_id": 16369,
"hgvs_c": "c.233G>A",
"hgvs_p": "p.Arg78Gln",
"transcript": "ENST00000377493.9",
"protein_id": "ENSP00000466242.1",
"transcript_support_level": 2,
"aa_start": 78,
"aa_end": null,
"aa_length": 169,
"cds_start": 233,
"cds_end": null,
"cds_length": 510,
"cdna_start": 291,
"cdna_end": null,
"cdna_length": 795,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PARK7",
"gene_hgnc_id": 16369,
"hgvs_c": "c.176G>A",
"hgvs_p": "p.Arg59Gln",
"transcript": "ENST00000469225.1",
"protein_id": "ENSP00000466756.1",
"transcript_support_level": 3,
"aa_start": 59,
"aa_end": null,
"aa_length": 160,
"cds_start": 176,
"cds_end": null,
"cds_length": 483,
"cdna_start": 176,
"cdna_end": null,
"cdna_length": 711,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PARK7",
"gene_hgnc_id": 16369,
"hgvs_c": "c.293G>A",
"hgvs_p": "p.Arg98Gln",
"transcript": "XM_005263424.4",
"protein_id": "XP_005263481.1",
"transcript_support_level": null,
"aa_start": 98,
"aa_end": null,
"aa_length": 189,
"cds_start": 293,
"cds_end": null,
"cds_length": 570,
"cdna_start": 687,
"cdna_end": null,
"cdna_length": 1415,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PARK7",
"gene_hgnc_id": 16369,
"hgvs_c": "n.453G>A",
"hgvs_p": null,
"transcript": "ENST00000460192.5",
"protein_id": null,
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 567,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PARK7",
"gene_hgnc_id": 16369,
"hgvs_c": "n.362G>A",
"hgvs_p": null,
"transcript": "ENST00000465354.5",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 949,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PARK7",
"gene_hgnc_id": 16369,
"hgvs_c": "n.312G>A",
"hgvs_p": null,
"transcript": "ENST00000497113.1",
"protein_id": null,
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 670,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PARK7",
"gene_hgnc_id": 16369,
"dbsnp": "rs71653619",
"frequency_reference_population": 0.009320799,
"hom_count_reference_population": 104,
"allele_count_reference_population": 15045,
"gnomad_exomes_af": 0.00954739,
"gnomad_genomes_af": 0.00714539,
"gnomad_exomes_ac": 13957,
"gnomad_genomes_ac": 1088,
"gnomad_exomes_homalt": 99,
"gnomad_genomes_homalt": 5,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.007415413856506348,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.202,
"revel_prediction": "Benign",
"alphamissense_score": 0.1402,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.26,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 5.372,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0,
"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": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BS1,BS2",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000338639.10",
"gene_symbol": "PARK7",
"hgnc_id": 16369,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.293G>A",
"hgvs_p": "p.Arg98Gln"
}
],
"clinvar_disease": "Autosomal recessive early-onset Parkinson disease 7,PARK7-related disorder,Renal cysts and diabetes syndrome,not provided,not specified",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:4 B:4",
"phenotype_combined": "not provided|Autosomal recessive early-onset Parkinson disease 7|Renal cysts and diabetes syndrome|not specified|PARK7-related disorder",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}